Citrullinated peptides for diagnosing and prognosing rheumatoid arthritis

ABSTRACT

The present invention provides novel citrullinated peptides, their use in methods for aiding, assisting, improving, or facilitating the diagnosis or prognosis of rheumatic diseases such as rheumatoid arthritis (RA), and methods for identifying novel citrullinated peptides that are immunoreactive with anti-citrullinated protein antibodies (ACPAs). The present invention also provides methods for detecting rheumatoid factor (RF) using novel RF detection reagents as a means to aid, assist, improve, or facilitate the diagnosis or prognosis of rheumatic diseases such as RA. Kits comprising at least one of the novel citrullinated peptides and/or RF detection reagents of the present invention are also provided.

CROSS-REFERENCES TO RELATED APPLICATIONS

The present application is a divisional of U.S. patent application Ser.No. 13/239,329, filed Sep. 21, 2011, which is a continuation ofPCT/US2010/028946, filed Mar. 26, 2010, which application claims thebenefit of priority to U.S. Provisional Patent Application Nos.61/164,840, filed Mar. 30, 2009; 61/243,496, filed Sep. 17, 2009; and61/255,058, filed Oct. 26, 2009, the disclosures of which are herebyincorporated by reference in their entirety for all purposes.

REFERENCE TO A “SEQUENCE LISTING,” A TABLE, OR A COMPUTER PROGRAMLISTING APPENDIX SUBMITTED AS AN ASCII TEXT FILE

The Sequence Listing written in file -152-3, TXT, created on Jul. 2,2012, 434,176 bytes, machine format IBM-PC, MS-Windows operating system,is hereby incorporated by reference in its entirety for all purposes.

BACKGROUND OF THE INVENTION

Rheumatoid arthritis (RA) is a chronic inflammatory disease, generallyregarded as an autoimmune disorder, that affects approximately 1% of theadult population. It is characterized primarily by inflammation of theperipheral joints, in many cases ultimately leading to destruction ofthese joints. However, RA is a systemic disease, as especiallylong-standing (and severe) cases also develop extra-articularmanifestations of symptoms. As the structural damage is progressive andlargely irreversible, it is important to diagnose RA as early aspossible to be able to start an adequate treatment. This holdsespecially true for patients at risk of or having severe RA, which ischaracterized, for example, by increased joint destruction (as measuredby a higher radiological progression rate).

RA is caused by Chronic Inflammation of the Synovium that does not heal(Firestein, Nature, 423:356-361 (2003)). The synovium is a thin layer oftissue composed of 3 to 4 layer of cells that form a membraneencapsulating the joint fluid in a synovial joint (Iwanaga et al., Arch.Histol. Cytol., 63:17-31 (2000)). Chronic inflammation of the synoviumleads to unchecked proliferation of the synovial tissue, which iscomposed mainly of two types of cells, the A cells which aremacrophage-like and the B cells which are fibroblast-like (Iwanaga etal., supra). The outgrowth of the proliferating synovium into the jointcavity causes swelling of the joint and the formation of a destructivepiece of hanging tissue called the “Pannus” (Sanchez-Pernaute et al.,Rheumatology, 42:19-25 (2003)). It is the Pannus which acts like a“warhead” of a missile that does most of the damage to the articularcartilage by the generation and secretion of the matrixmetalloproteinases (MMPs) that break up the cartilage matrix proteins inthe joint (Pap et al., Arthritis Res., 2:361-367 (2000); Konttinen etal., Matrix Biology, 17:585-601 (1998)). Once the cartilage starts toerode, the disease becomes very serious because joint swelling and painstarts to develop which is the hallmark of RA (Firestein, Nature,423:356-361 (2003)).

However, several fundamental questions on the etiology of RA remain. Itis still unknown what mechanism initiates the inflammation in thesynovium, and similarly, what mechanism sustains the chronicinflammation in the synovium. What is known, is that chronicinflammation in any bodily tissue has to be driven and sustained by thecontinuous presence of a foreign antigen (or antigens) in the inflamedtissue. Unfortunately, no animal models of arthritis can truly mimic thechronic inflammatory condition of RA because the so-called“collagen-induced arthritis”, “albumen-induced arthritis” and “bacterialcell wall-induced arthritis” animal models of arthritis (Brahn Clin.Orthop. Relat. Res., 265:42-53 (1991)) are all acute animal models, asthe arthritic disease is induced by immunizing the animals with asubcutaneous injection of the antigen mixed with Freund's completeadjuvant and then followed later by an injection of the antigen into thesynovial joint cavity in one of the knees of the animal while thenon-injected knee serves as the control. After the injection, arthriticdisease will develop in the injected knee joint within a week while thenon-injected knee joint is disease-free. However, appearance of thedisease is only transient because the diseased joint will eventuallyheal itself and the animal recovers spontaneously. This phenomenonoccurs because the antigen that causes the disease is no longer presentin the diseased joint to sustain the disease. As such, in all of theanimal models of arthritis, the antigen that induces the disease isdelivered exogenously by manual injection into the joint cavity. Thus,in order to properly diagnose and treat RA it is of paramount importanceto determine what mechanism(s) are responsible for generating andsustaining a continuous presence of one or more foreign antigens, aswell as the identity of the foreign antigen(s) underlying the disease.

Due to the tremendous research efforts executed by numerous laboratoriesall over the world in the past 15 years, researchers believe that theforeign antigen (or antigens) responsible for inducing and sustaining RAin RA-prompt patients are the citrulline-containing peptides derivedfrom citrullination of the endogenous cellular proteins by theintracellular enzymes, peptidyl-arginine deiminases (PADs) (Schellekenset al., J. Clin. Invest., 101:273-281 (1998); Girbal-Neuhauser et al.,J. Immunol., 162:585-594 (1999)). PADs convert an arginine residuewithin a peptide sequence to a citrulline residue and this reaction onlyoccurs in the presence of >10⁻⁴M Ca²⁺ concentration. There are fiveknown members of PADs (I, II, III, IV and VI) present inside the cells,and PADs II and IV are the ones found in the synovial cells (Foulquieret al., Arthritis & Rheumatism, 56:3541-3553 (2007)). Once a PAD isreleased outside of the cell, it can citrullinate other extracellularproteins but the enzymatic activity also disappears rapidly. Therefore,to further explore the cause of RA, one has to determine how thecitrullinated peptides are being generated in the synovium and whatsustains the continuous generation of those citrullinated peptides.

A correct diagnosis of RA is often difficult because the symptomsdevelop insidiously, or may resemble those of other diseases (e.g.,osteoarthritis, arthritis due to infection or gout, etc.).Traditionally, RA is diagnosed using the revised American College ofRheumatology (ACR) classification criteria. The ACR proposes sevenclassification criteria which indicate a poor prognosis:

-   -   1. Morning stiffness of the joints lasting more than one hour;    -   2. Arthritis of three or more joints;    -   3. Inflammation of at least three joint areas at the same time;    -   4. Hand joints or finger joints are likewise affected;    -   5. Bilateral tenderness of metacarpophalangeal joints to        pressure;    -   6. Erosions on radiographs;    -   7. Detection of rheumatoid factors, anti-perinuclear factor        (APF), and anti-keratin antibodies (AKA).        However, diagnosing RA according to this procedure is        labor-intensive and a significant amount of time passes before a        definite diagnosis is made.

Autoantibodies to the “anti-perinuclear factor” (APF) were firstdescribed by Nienhuis et al. in patients having rheumatoid arthritis(Nienhuis et al., Ann. Rheum. Dis., 23:302-305 (1964)). These APFantibodies react with the keratohyaline scattered around the perinuclearregion of human buccal epithelial cells. Owning to the subjective andlabor-intensive immunofluorescence technique employed, an APF antibodytest has never been put into wide use for RA diagnosis. Later, Young etal. reported that RA patient sera reacted to the keratinous epitheliumof the stratum corneum on rat esophagus tissue sections and designatedthese RA-specific antibodies as anti-keratin antibodies (AKA) (Young etal., B.M.J., 2:97-99 (1979)). In 1993, Simon et al. found that amajority of the RA patient sera recognized a 40 kDa protein from humanskin tissue (Simon et al., J. Clin. Invest., 92:1387-93 (1993)). Theyfurther demonstrated that this protein identified as filaggrin was thetarget antigen of AKA and went on to show that AKA and APF antibodiesare the same RA-specific antibodies (Sebbag et al., J. Clin. Invest.,95:2672-2679 (1995)). For this reason, the APF autoantibodies are eventoday referred to as antikeratin antibodies (AKAs) (Vincent et al., J.of Autoimmunity, 4:493-505 (1991); Paimela et al., Ann. Rheumat. Dis.,51:743-746 (1992)). The 40 kDa filaggrin protein aggregates cytokeratinfilaments and assists in forming the intracellular fiber matrix of thekeratinous cells (Simon et al., J. Clin. Invest., 92:1387-93 (1993)).However, filaggrin is not present in the synovial joint tissue of RApatients. Furthermore, anti-filaggrin antibodies are found in the serumof only about 40% of RA patients.

As such, there is a need in the art for the identification and design ofnovel peptides that find utility in detecting antibodies associated withrheumatic diseases, e.g., antibodies associated with RA, which peptidesmake possible a sensitive and specific diagnosis, classification, and/orprognosis of rheumatic diseases such as RA. The present inventionsatisfies this need and provides related advantages as well.

BRIEF SUMMARY OF THE INVENTION

The present invention provides novel citrullinated peptides, their usein methods for aiding, assisting, improving, or facilitating thediagnosis or prognosis of rheumatic diseases such as rheumatoidarthritis (RA), and methods for identifying novel citrullinated peptidesthat are immunoreactive with anti-citrullinated protein antibodies(ACPAs). The present invention also provides methods for detectingrheumatoid factor (RF) using novel RF detection reagents as a means toaid, assist, improve, or facilitate the diagnosis or prognosis ofrheumatic diseases such as RA. Kits comprising at least one of the novelcitrullinated peptides and/or RF detection reagents of the presentinvention are also provided.

The compositions and methods of the present invention are advantageousbecause they make possible the early diagnosis of RA, and provideimportant prognostic information regarding the course of the disease(e.g., early stage, middle stage, and late stage) and the recommendedtherapy at the time of diagnosis. As such, the present invention enablesa clinician to practice “personalized medicine” by guiding treatmentdecisions for RA such that the right drug is given to the right patientat the right time.

In one aspect, the present invention provides a synthetic peptidecomprising a fragment of about 5 to about 50 contiguous amino acids of ahuman protein selected from the group consisting of SEQ ID NOS:1-39,wherein at least one of the contiguous amino acids is an arginineresidue in the native protein, and wherein at least one of the arginineresidues is citrullinated in the synthetic peptide.

In another aspect, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of a human protein selected from the group consisting of SEQ IDNOS:1-39 linked to at least a second fragment of about 5 to about 50contiguous amino acids of a human protein selected from the groupconsisting of SEQ ID NOS:1-39, wherein at least one residue of the firstfragment is an arginine residue in the native protein and at least oneresidue of the second fragment is an arginine residue in the nativeprotein, and wherein at least one of the arginine residues in the firstand/or second fragments is citrullinated in the synthetic peptide.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NOS:1-39, wherein at least one residueof each of the third or fourth fragments is an arginine residue in thenative protein, and wherein the third or fourth fragments are linked tothe first and second fragments, e.g., by a peptide bond.

In yet another aspect, the present invention provides a syntheticpeptide comprising a first synthetic fragment of about 5 to about 50amino acids having homology to a first fragment of about 5 to about 50contiguous amino acids of a human protein selected from the groupconsisting of SEQ ID NOS:1-39 linked to at least a second (andoptionally a third or fourth) synthetic fragment of about 5 to about 50amino acids having homology to a second (and optionally third or fourth)fragment of about 5 to about 50 contiguous amino acids of a humanprotein selected from the group consisting of SEQ ID NOS:1-39, whereinat least one residue of the first synthetic fragment is an arginineresidue in the human protein and at least one residue of the second (andoptionally third or fourth) synthetic fragment is an arginine residue inthe human protein, wherein at least one of the arginine residues iscitrullinated in the synthetic peptide, and wherein the composite aminoacid sequence of the first synthetic fragment and the second (andoptionally third or fourth) synthetic fragment is at least about 85%,90%, 95%, or more identical to the composite amino acid sequence of thefirst and second fragments of the human protein.

In particular embodiments, the human protein is vimentin (SEQ ID NO:1),and the synthetic peptide comprises one or more fragments independentlyselected from the group consisting of amino acid residues 2-13, 4-12,22-31, 28-38, 42-52, 61-70, 63-78, 68-76, 96-104, 116-124, 158-165,157-165, 205-217, 216-224, 266-276, 320-328, 302-327, 356-364, 393-412,and 417-452 of SEQ ID NO:1, wherein the fragments are linked together(e.g., by a peptide bond), and wherein at least one of the arginineresidues in each of the fragments is citrullinated.

In another aspect, the present invention provides synthetic peptidescomprising an amino acid sequence selected from the group consisting ofSEQ ID NOS:40-355. In certain embodiments, the synthetic peptides of theinvention may be labeled, tagged, amidated, or otherwise chemicallymodified.

In a related aspect, the present invention provides synthetic peptidescomprising an amino acid sequence that is at least about 85%, 90%, 95%,or more identical to a sequence selected from the group consisting ofSEQ ID NOS:40-355. In certain embodiments, the synthetic peptides may belabeled, tagged, amidated, or otherwise chemically modified.

In some embodiments, the synthetic peptide comprises an amino acidsequence selected from the group consisting of SEQ ID NOS:41, 43, 45,47, 49, 51, 53, 55, 57, 59, 61, 63, 65, and 67. In other embodiments,the synthetic peptide comprises an amino acid sequence that is at leastabout 85%, 90%, 95%, or more identical to an amino acid sequenceselected from the group consisting of SEQ ID NOS:41, 43, 45, 47, 49, 51,53, 55, 57, 59, 61, 63, 65, and 67. In yet other embodiments, thesynthetic peptide is selected from the group consisting of SEQ IDNOS:40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, and 66.

In yet another aspect, the present invention provides a method fordetecting an anti-citrullinated protein antibody in a biological sample,the method comprising the steps of:

-   -   (a) contacting the biological sample with a synthetic peptide        described herein under conditions suitable to transform said        synthetic peptide into a complex comprising the synthetic        peptide and the anti-citrullinated protein antibody; and    -   (b) detecting the presence (or absence) or level of the complex.

In another aspect, the present invention provides a method forperforming an assay to aid in the diagnosis or prognosis of rheumatoidarthritis, the method comprising:

-   -   (a) detecting the presence (or absence) or level of an        anti-citrullinated protein antibody in a biological sample by        contacting the sample with a synthetic peptide described herein;        and    -   (b) reporting the presence (or absence) or level of the        anti-citrullinated protein antibody in the sample to aid in the        diagnosis or prognosis of rheumatoid arthritis.

In a related aspect, the present invention provides a method forimproving the sensitivity of diagnosing or prognosing rheumatoidarthritis, the method comprising:

-   -   (a) detecting the presence (or absence) or level of an        anti-citrullinated protein antibody in a biological sample by        contacting the sample with a synthetic peptide described herein;        and    -   (b) reporting the presence (or absence) or level of the        anti-citrullinated protein antibody in the sample to improve the        sensitivity of diagnosing or prognosing rheumatoid arthritis.

In a related aspect, the present invention provides an assay fordiagnosing or prognosing rheumatoid arthritis, the assay comprising:

-   -   (a) contacting a biological sample with a synthetic peptide        described herein under conditions suitable to transform the        synthetic peptide into a complex comprising the synthetic        peptide and an anti-citrullinated protein antibody; and    -   (b) detecting the presence (or absence) or level of the complex.

In yet another aspect, the present invention provides a kit comprising:

-   -   (a) at least one synthetic peptide described herein; and    -   (b) at least one detectable moiety.

In another aspect, the present invention provides a method foridentifying a peptide that is immunologically reactive with ananti-citrullinated protein antibody, the method comprising:

-   -   (a) identifying at least one antigenic peptide epitope in at        least one synovial fluid polypeptide, wherein the antigenic        peptide epitope is predicted to be immunologically reactive with        an anti-citrullinated protein antibody, wherein the antigenic        peptide epitope contains at least one citrullinated arginine        residue;    -   (b) synthesizing a peptide that comprises at least one of the        antigenic peptide epitopes;    -   (c) contacting a biological sample from a rheumatoid arthritis        (RA) individual with the peptide under conditions suitable to        transform the peptide into a complex comprising the peptide and        the anti-citrullinated protein antibody; and    -   (d) identifying the peptide as being immunologically reactive        with the anti-citrullinated protein antibody based on the        presence of the complex.

Other objects, features, and advantages of the present invention will beapparent to one of skill in the art from the following detaileddescription and figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates the different stages of rheumatoid arthritis (RA) andan overview of autoantibody profiling in RA.

FIG. 2A illustrates a dose-response curve for the citrullinatedvimentin-peptide VMT1 using an ELISA to detect the presence or level ofanti-citrullinated protein antibodies (“ACPAs”). FIG. 2B illustrates adose-response curve for the citrullinated vimentin-peptide VMT2 using anELISA to detect the presence or level of ACPAs. FIG. 2C illustrates adose-response curve for the citrullinated vimentin-peptide VMT3 using anELISA to detect the presence or level of ACPAs. FIG. 2D illustrates adose-response curve for the citrullinated vimentin-peptide VMT4 using anELISA to detect the presence or level of ACPAs. FIG. 2E illustrates adose-response curve for the citrullinated vimentin-peptide VMT5 using anELISA to detect the presence or level of ACPAs.

FIG. 3 illustrates a comparison of the dose-response curves for thecitrullinated vimentin peptides shown in Table 1 using an ELISA todetect the presence or level of ACPAs.

FIG. 4A illustrates the dose-response curve for the [Arg²⁵]Cit-α32peptide using an ELISA to detect the presence or level of IgG ACPAs.FIG. 4B illustrates a comparative dose-response curve using the cycliccitrullinated peptide (CCP) IgG assay from INOVA Diagnostics, Inc.

FIG. 5 illustrates a comparison of the IgG ACPA values obtained usingthe NOVA CCP assay versus the [Arg²⁵]Cit-α32 peptide assay for normalhuman serum (NHS) and RF-positive (C) samples.

FIG. 6 illustrates the dose-response curves for the [Arg²⁵]Cit-α32peptide using an ELISA to detect the presence or level of IgA, IgG, IgM,or IgA/G/M ACPAs.

FIG. 7 illustrates the dose-response curves for additional citrullinatedfibrinogen alpha-chain peptides of the invention using an ELISA todetect the presence or level of ACPAs. FIG. 7 also illustrates thedose-response curves for citrullinated fibrinogen beta-chain peptides ofthe invention using an ELISA to detect the presence or level of ACPAs.

FIG. 8A illustrates the dose-response curve for HRP-labeled Protein Lusing an ELISA to detect the presence or level of RF. FIG. 8Billustrates a comparative dose-response curve using a kit from OrgentecDiagnostika GmbH.

FIG. 9 illustrates a comparison of the RF values obtained using theOrgentec RF assay versus the inventive Protein L assay for normal humanserum (NHS) and RF-positive samples (C).

FIG. 10 illustrates an exemplary peptide epitope side-chain scanningtable suitable for use in the prediction and design of novelcitrullinated peptides.

FIG. 11 illustrates how the score of a selected 9-residue peptide (SEQID NOS:357-365) epitope in the vimentin polypeptide (SEQ ID NO:356) inwhich an arginine was replaced with glutamine is determined by the RAantigenic peptide prediction program of the present invention.

FIG. 12 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in the vimentinamino acid sequence (SEQ ID NO:1), wherein the arginines were replacedwith glutamine.

FIG. 13 illustrates non-limiting examples of synthetic peptides (SEQ IDNOS:366-374) having composite amino acid sequences derived from highscoring vimentin peptide epitopes (≧+2.0), which were determined by theRA antigenic peptide prediction program of the present invention.“X”=citrulline.

FIG. 14 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in thefibrinogen alpha-chain amino acid sequence (SEQ ID NO:2), wherein thearginines were replaced with glutamine.

FIG. 15 illustrates non-limiting examples of synthetic peptides (SEQ IDNOS:375-382) having composite amino acid sequences derived from highscoring fibrinogen alpha-chain peptide epitopes (≧+2.0), which weredetermined by the RA antigenic peptide prediction program of the presentinvention. “X”=citrulline.

FIG. 16 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in thefibrinogen beta-chain amino acid sequence (SEQ ID NO:3), wherein thearginines were replaced with glutamine.

FIG. 17 illustrates non-limiting examples of synthetic peptides (SEQ IDNOS:383-385) having composite amino acid sequences derived from highscoring fibrinogen beta-chain peptide epitopes (≧+2.0), which weredetermined by the RA antigenic peptide prediction program of the presentinvention. “X”=citrulline.

FIG. 18 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in thealpha-enolase amino acid sequence (SEQ ID NO:5), wherein the arginineswere replaced with glutamine.

FIG. 19 illustrates non-limiting examples of synthetic peptides (SEQ IDNOS:386-388) having composite amino acid sequences derived from highscoring alpha-enolase peptide epitopes (≧+2.0), which were determined bythe RA antigenic peptide prediction program of the present invention.“X”=citrulline.

FIG. 20 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from Apolipoprotein a.

FIG. 21 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from collagen (e.g., Coll.T2α1,Coll.T9α1, Coll.T10α1, Coll.T11α1, and Coll.T11α2).

FIG. 22 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from vimentin.

FIG. 23 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from fibronectin.

FIG. 24 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from fibrin (e.g., fibrin alpha-chain,beta-chain, and gamma-chain).

FIG. 25 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from alpha-enolase and syndecan.

FIG. 26 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from histone, β-actin, and PL scramblase.

FIG. 27 illustrates the IgG ACPA dose-response curve of syntheticcitrullinated peptides derived from myeloblastin, BiP, and lamin (e.g.,lamin B1, B2, and A/C)

DETAILED DESCRIPTION OF THE INVENTION I. Introduction

Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease.Currently, the prevalence of RA is estimated at 1% of the U.S.population; 3 million adults in the U.S. have been diagnosed with RA. Ifnot adequately managed, progressive deformity can lead to jointreplacement surgery. In the U.S. in 1997 alone, there were 256,000 kneereplacements and 117,000 hip replacements associated with arthritis.However, the clinical presentation and outcomes vary greatly amongdifferent patients.

One of the first reactions to an inflammatory insult, such as a viral orbacterial infection, or a minor tissue damage is the massive influx ofthe white blood cells to the injured area from the capillaries to repairthe damage and the influx is facilitated by the release of TNFα by theimmune surveillance cells (Moisan et al., J. Leukoc. Biol., 79:489-498(2006)). Over 60% of the granulocytes in the white blood cells incirculation are neutrophils, whose function is to phagocytize theviruses, bacteria and damaged tissues to clean up the damage area.However, in so doing, these “well-fed” neutrophils trapped in theextracellular matrix of the synovium also die there by “spontaneousapoptosis” (SA) and the apoptotic process is also induced by TNFα(Moisan et al., supra). When the neutrophils undergo SA, it lets in theextracellular Ca²⁺, which is present at 10⁻³ M concentration, into thecytoplasm of the cells where the Ca²⁺ concentration is normallymaintained at 10⁻⁶ M to inhibit the enzymatic activity of theintracellular peptidyl-arginine deiminases (PADs). Once theintracellular PADs are activated by the influx of Ca²⁺, they start tocitrullinate the endogenous intermediate filament proteins, such asvimentin and lamin B1 as well as other intracellular proteins such asthe histones and the heat shock protein, BiP (Moisan et al., supra).Moreover, in the process of being citrullinated, these normallyintracellular intermediate filament proteins, vimentin and lamin B1, aretranslocated to the cell surface and thus are being exposed forphagocytosis by the resident macrophages (the A cells in the synovium),which can serve as antigen presenting cells (APCs) for potentialgeneration of autoantibodies against these citrullinated proteins.

To induce antibody formation against an antigen in human beings, theantigen has to be bound to an allele-specific major histocompatibilitycomplex (MHC) class II molecule expressed on the APC's cell surface. Thebound antigenic peptide in the MHC-II complex is then recognized by areceptor on the CD4 helper T_(H2) cells (Yvonne Jones et al., NatureReviews/Immunology, 6:271-282 (2006)). Most RA-prompt patients expressthe MHC-II molecule, HLA-DR4, which can bind the citrullinated peptides(Yvonne Jones et al., supra), whereas non-RA-prompt human beings do notexpress this MHC-II molecule on their APCs. Therefore, in non-RA-prompthuman beings, neutrophil SA does not cause RA because the citrullinatedpeptides are not being presented by the APCs to the helper T_(H2) cellsdue to the absence of the MHC-II allele, HLA-DR4, and the inflammationis resolved. However, in the RA-prompt patients the MHC-II allele,HLA-DR4, is able to bind and present the bound citrullinated peptides toactivate the CD4 helper T_(H2) cells to induce antibody formationagainst these citrullinated peptides. And because of a special propertyof the synovial fibroblast-like cells (the B cells in the synovium), thesynovium acts like the germinal center of the lymph node to fosteractivated T_(H2) and B cells interaction to induce maturation of theactivated B cells to differentiate into plasma cells to produce andsecrete the anti-citrullinated peptide autoantibodies to drive thedisease into a self-perpetuating inflammatory process (Dechanet et al.,J. Clin. Invest., 95:456-463 (1995); Edwards, Clin. Exp. Immunol.,108:407-414 (1997)). The self-perpetuating process is sustained by thebinding of the locally generated autoantibodies to the citrullinatedpeptide epitopes translocated to the surface of the apoptoticneutrophils to form immune complexes. These immune complexes, in turn,attract more naive neutrophils from the circulation to carry out thephagocytosis, followed by SA to repeat the inflammatory cycle. When thedisease develops to this chronic stage, fibrin aggregates start toappear inside the joint cavity and adhere to the synovial lining(Sanchez-Pernaute et al., Rheumatology, 42:19-25 (2003)). The adheredfibrin aggregates, in turn, trigger an invasion by the synovialfibroblasts, ending with the complete incorporation of the aggregateswithin the tissue by development of a new lining layer at their surfaceand this is how a Pannus tissue develops (Sanchez-Pernaute et al.,supra). At this stage, many citrullinated autoantibodies against othercellular and extracellular matrix proteins will appear in the patientbecause, in addition to neutrophil SA, other immune cells, such asmacrophages and even fibroblasts will also undergo apoptosis and releasemassive amounts of PADs to citrullinate other proteins for autoantibodygeneration and this is how the phenomenon of epitope spreading occurs(Kidd et al., Arthritis Res. Ther., 10:R119 (2008)). However, thesespreading epitopes are not useful as diagnostic peptides for thedetection of early RA because, when autoantibodies against thesespreading epitopes start to appear, the disease has already progressedto a very serious stage, which may not be treatable with an anti-TNFαagent.

Therefore, in order to effectively treat RA, the disease should bediagnosed in its early stage by detecting the presence ofanti-citrullinated intermediate filament proteins, vimentin and lamin B1as well as, possibly, anti-citrullinated histone and BiP peptideautoantibodies in the patient serum and treat the patient immediatelywith an anti-TNFα agent to block the early inflammatory process. If theearly inflammatory process is inhibited, the inflammation will beresolved and the patient will not proceed to develop RA a few yearslater. Moreover, the healthy status of the patient can be monitored bymeasuring the reappearance of the anti-citrullinated vimentin, lamin B1,histone and BiP autoantibodies in the serum. If these antibodiesreappear, the patient can be treated with an anti-TNFα agent again toresolve the inflammation.

Thus, the heterogeneity in RA could be explained by the differentautoantibodies against citrullinated synovial fluid proteins present ina patient. It has been discovered that the antigenic peptide whichinduces autoantibodies in RA patients contains an arginine residue thatis transformed to citrulline by the endogenous enzyme PAD (Schellekenset al., J. Clin Invest., 101:273-281 (1998); Girbal-Neuhauser et al., J.Immunol., 162:585-594 (1999)). For example, one-half of RA patients whohad the disease for more than 10 years had autoantibodies against thecitrullinated β- and γ-chains of fibrin (Zhao et al., Arthritis Res. &Ther., 10:R94 (2008)). However, current methods for detectingautoantibodies against citrullinated peptides are low in sensitivity andare unable to diagnose all stages of RA, especially early RA.

Currently, a citrullinated and mutated, recombinant vimentin ELISA,marketed by Orgentec, is the only RA diagnostic assay that can predictthe severe outcome in patients with recent-onset polyarthritis (Mathssonet al., Arthritis & Rheumatism, 58: 36-45 (2008)), whereas the anti-CCPassay does not have this capability. However, the sensitivity of theOrgentic assay is less than 30%. The reason for the low sensitivity ofthis assay is because citrullinated vimentin is only one of thecitrullinated proteins produced during SA of the neutrophils.Advantageously, the present invention provides, in one aspect, acomputer program that can predict all of the potential citrullinated RAepitopes in any cellular protein. Through the use of this program, allof the citrullinated vimentin, lamin B1, as well as other intermediatefilament-derived peptides can be predicted, for custom synthesis for useas autoantigens to detect the citrullinated peptide autoantibodiespresent in early RA patients. Thus, the present invention also providesa comprehensive assay containing a plurality of autoantigens generatedin neutrophil SA, resulting in higher sensitivity for the earlydetection of RA.

FIG. 1 illustrates the different stages of RA and the use of the novelcitrullinated peptides identified and designed in accordance with thepresent invention to provide valuable diagnostic and prognosticinformation for patients with any stage of RA, including early RA. Inparticular, autoantibody profiling using one or more (e.g., a pool) ofthe synthetic peptides described herein advantageously (1) enables thescreening of patients at risk of developing RA, (2) facilitates earlydiagnosis and prognosis of RA, (3) enables the selection of optimaltherapy or the monitoring of therapeutic efficacy in RA patients, (4)enables the prevention of the progression of RA, and (5) enables theidentification of the need for surgical intervention in RA patients.

As such, the compositions and methods of the present invention makepossible the early diagnosis of RA, and provide important prognosticinformation regarding the course of the disease and the recommendedtherapy at the time of diagnosis. For example, patients diagnosed withearly RA and with a good prognosis may be recommended non-steroidalanti-inflammatory drug (NSAID) therapy, whereas patients diagnosed withearly RA, but with a poor prognosis may be recommended disease-modifyingantirheumatic drug (DMARD) therapy. In some embodiments, the presentinvention enables the classification of RA patients into differentsubsets and provides guidance on therapy selection based on the subsetof RA. In other embodiments, the present invention enables themonitoring of a patient's response to treatment and provides guidance onthe selection of the appropriate therapy or combination therapy for thepatient. In particular, the present invention finds utility in guidingtreatment decisions (e.g., which therapy to select, when that therapyshould begin and end, etc.) to increase the likelihood of efficacy anddecrease the likelihood of toxicity and failure since RA therapy is veryexpensive. Accordingly, the present invention enables a clinician topractice “personalized medicine” by guiding treatment decisions forrheumatic diseases such that the right drug is given to the rightpatient at the right time.

II. Definitions

As used herein, the following terms have the meanings ascribed to themunless specified otherwise.

The term “rheumatoid arthritis” or “RA” includes an autoimmune diseasethat causes chronic inflammation of the connective tissues in the body,most particularly, the joints and the tissue around the joints. Inrheumatoid arthritis, multiple joints are usually inflamed in asymmetrical pattern (e.g., both sides of the body are affected). Thesmall joints of both the hands and wrists as well as the feet are ofteninvolved. More rarely, the cricoarytenoid joint is involved, causing ahoarseness of the voice. The term “rheumatoid arthritis” also includesconditions such as Sjogren's syndrome, where the inflammation affectsorgans and areas of the body other than the joints, e.g., the glands ofthe eyes and mouth, causing dryness of these areas. Rheumatoidinflammation of the lung lining (pleuritis) causes chest pain with deepbreathing or coughing. The lung tissue itself can also become inflamedand sometimes nodules of inflammation (rheumatoid nodules) developwithin the lungs. Inflammation around the heart (pericarditis) can causea chest pain that typically changes in intensity when lying down orleaning forward. Rheumatoid arthritis can reduce the number of red bloodcells (anemia) and white blood cells. Decreased white blood cells can beassociated with an enlarged spleen (referred to as Felty's syndrome) andcan increase the risk of infections. Firm lumps under the skin(rheumatoid nodules) can occur around the elbows and fingers where thereis frequent pressure. Even though these nodules usually do not causesymptoms, occasionally they can become infected. A rare, seriouscomplication, usually with long-standing rheumatoid disease, is bloodvessel inflammation (vasculitis). Vasculitis can impair blood supply totissues and lead to tissue death. This is most often initially visibleas tiny black areas around the nail beds or as leg ulcers.

The term “rheumatoid factor” or “RF” includes an autoantibody (i.e., anantibody directed against an organism's own tissues) that is typicallydirected against (i.e., binds to) the Fc (fragment crystallizable)portion of immunoglobulin G (IgG). Rheumatoid factor is most often anIgM autoantibody, but may also be an IgG or IgA autoantibody.

The term “anti-citrullinated protein antibody,” “anti-citrullinatedpeptide antibody,” or “ACPA” includes an autoantibody that specificallytargets one or more epitopes in a peptide, polypeptide, or proteinsequence where one or more arginine residues have been converted by theenzyme peptidylarginine deiminase into a citrulline residue during apost-translational modification. The presence or level ofanti-citrullinated protein antibodies can be detected, determined, ormeasured using the natural or synthetic citrullinated peptides of thepresent invention, which are immunologically reactive (i.e.,immunoreactive) with such antibodies. Anti-citrullinated proteinantibodies are autoantibodies typically associated with rheumatoidarthritis.

The term “subject,” “patient,” or “individual” typically includeshumans, but can also include other animals such as, e.g., otherprimates, rodents, canines, felines, equines, ovines, porcines, and thelike.

The term “amino acid” includes naturally-occurring α-amino acids andtheir stereoisomers, as well as unnatural amino acids and theirstereoisomers. “Stereoisomers” of amino acids refers to mirror imageisomers of the amino acids, such as L-amino acids or D-amino acids. Forexample, a stereoisomer of a naturally-occurring amino acid refers tothe mirror image isomer of the naturally-occurring amino acid, i.e., theD-amino acid.

Naturally-occurring amino acids are those encoded by the genetic code,as well as those amino acids that are later modified, e.g., citrulline(Cit), γ-aminoglutamic acid, or O-phosphoserine. Naturally-occurringα-amino acids include, without limitation, alanine (Ala), cysteine(Cys), aspartic acid (Asp), glutamic acid (Glu), phenylalanine (Phe),glycine (Gly), histidine (His), isoleucine (Ile), arginine (Arg), lysine(Lys), leucine (Leu), methionine (Met), asparagine (Asn), proline (Pro),glutamine (Gln), serine (Ser), threonine (Thr), valine (Val), tryptophan(Trp), tyrosine (Tyr), and combinations thereof. Stereoisomers of anaturally-occurring α-amino acids include, without limitation, D-alanine(D-Ala), D-cysteine (D-Cys), D-aspartic acid (D-Asp), D-glutamic acid(D-Glu), D-phenylalanine (D-Phe), D-histidine (D-His), D-isoleucine(D-Ile), D-arginine (D-Arg), D-lysine (D-Lys), D-leucine (D-Leu),D-methionine (D-Met), D-asparagine (D-Asn), D-proline (D-Pro),D-glutamine (D-Gln), D-serine (D-Ser), D-threonine (D-Thr), D-valine(D-Val), D-tryptophan (D-Trp), D-tyrosine (D-Tyr), and combinationsthereof.

Amino acids may be referred to herein by either their commonly knownthree letter symbols or by the one-letter symbols recommended by theIUPAC-IUB Biochemical Nomenclature Commission. For example, an L-aminoacid may be represented herein by its commonly known three letter symbol(e.g., Arg for L-arginine) or by an upper-case one-letter amino acidsymbol (e.g., R for L-arginine). A D-amino acid may be representedherein by its commonly known three letter symbol (e.g., D-Arg forD-arginine) or by a lower-case one-letter amino acid symbol (e.g., r forD-arginine).

The term “substantially the same amino acid sequence” includes an aminoacid sequence that is similar, but not identical to, thenaturally-occurring amino acid sequence. For example, an amino acidsequence that has substantially the same amino acid sequence as anaturally-occurring peptide, polypeptide, or protein can have one ormore modifications such as amino acid additions, deletions, orsubstitutions relative to the amino acid sequence of thenaturally-occurring peptide, polypeptide, or protein, provided that themodified sequence retains substantially at least one biological activityof the naturally-occurring peptide, polypeptide, or protein such asimmunoreactivity. Comparison for substantial similarity between aminoacid sequences is usually performed with sequences between about 6 and100 residues, preferably between about 10 and 100 residues, and morepreferably between about 25 and 35 residues. A particularly usefulmodification of a peptide, polypeptide, or protein of the presentinvention, or a fragment thereof, is a modification that confers, forexample, increased stability. Incorporation of one or more D-amino acidsis a modification useful in increasing stability of a polypeptide orpolypeptide fragment. Similarly, deletion or substitution of lysineresidues can increase stability by protecting the polypeptide orpolypeptide fragment against degradation.

One of skill in the art will recognize that individual substitutions,additions, or deletions to a peptide, polypeptide, or protein sequencewhich alters, adds, or deletes a single amino acid or a small percentageof amino acids in the encoded sequence is a “conservatively modifiedvariant” where the alteration results in the substitution of an aminoacid with a chemically similar amino acid. The chemically similar aminoacid includes, without limitation, a naturally-occurring amino acid suchas an L-amino acid, a stereoisomer of a naturally-occurring amino acidsuch as a D-amino acid, and an unnatural amino acid such as an aminoacid analog, amino acid mimetic, synthetic amino acid, N-substitutedglycine, and N-methyl amino acid.

Conservative substitution tables providing functionally similar aminoacids are well known in the art. For example, substitutions may be madewherein an aliphatic amino acid (e.g., G, A, I, L, M, or V) issubstituted with another member of the group. Similarly, an aliphaticpolar-uncharged group such as C, S, T, N, or Q may be substituted withanother member of the group; and basic residues, e.g., K, R, or H, maybe substituted for one another. In some embodiments, an amino acid withan acidic side chain, e.g., E or D, may be substituted with itsuncharged counterpart, e.g., Q or N, respectively; or vice versa. Inother embodiments, aromatic amino acids (e.g., F, Y, or W) may besubstituted with another member of the group. Each of the followingeight groups contains other exemplary amino acids that are conservativesubstitutions for one another:

1) Alanine (A), Glycine (G);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);

7) Serine (S), Threonine (T); and

8) Cysteine (C), Methionine (M)

(see, e.g., Creighton, Proteins, 1993).

The term “peptide” includes a compound made up of a single chain of D-or L-amino acids or a mixture of D- and L-amino acids joined by peptidebonds. Generally, peptides are about 2 to about 100 (e.g., 2-100, 2-75,2-50, 5-50, 5-45, 5-40, 5-35, 5-30, 5-25, 10-50, 10-45, 10-40, 15-40,20-40, 10-30, 15-30, 20-30, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) amino acids inlength. In certain embodiments, the citrullinated peptides of thepresent invention comprise or consist of about 5 to about 50 contiguousamino acids of a wild-type polypeptide or protein sequence (e.g., SEQ IDNOS:1-39), wherein at least one of the arginine (Arg) residues presentin the sequence is citrullinated. In certain other embodiments, thecitrullinated peptides of the present invention comprise or consist ofabout 5 to about 50 (e.g., about 5 to about 25) contiguous amino acidsfrom two, three, four, or more regions (attached directly or via alinker) of a wild-type polypeptide or protein sequence (e.g., syntheticpeptides having a composite amino acid sequence of about 10 to about 50amino acids in length made up of fragments from SEQ ID NOS:1-39 linkedtogether by peptide bonds), wherein at least one of the Arg residuespresent in the synthetic peptide sequence is citrullinated. In furtherembodiments, the citrullinated peptides of the present inventioncomprise or consist of about 5 to about 50 contiguous amino acids of amutated version of a wild-type polypeptide or protein sequence (e.g.,peptides having one of the mutated vimentin sequences described in PCTPublication No. WO 07/000,320), wherein at least one of the Arg residuespresent in the sequence is citrullinated.

A “cyclic peptide” includes a peptide in which the amino-terminus of thepeptide or a side-chain on the peptide having a free amino group (e.g.,lysine) is joined by a peptide bond to the carboxyl-terminus of thepeptide or a side-chain on the peptide having a free carboxyl group(e.g., aspartic acid, glutamic acid). However, one skilled in the artwill appreciate that heterodetic cyclic peptides formed by disulfide,ester, or ether bonds are also within the scope of the presentinvention.

The term “sensitivity” includes the probability that an assay describedherein identifies a disease state (e.g., rheumatoid arthritis) amongthose who have the disease or the proportion of people with the diseasewho have a positive test result. Sensitivity can be expressed as thenumber of true positives/(the number of true positives+false negatives).

The term “specificity” includes the probability that an assay describedherein does not identify a disease state (e.g., rheumatoid arthritis)among those who do not have the disease or the proportion of people freeof the disease who have a negative test result. Specificity can beexpressed as the number of true negatives/(the number of truenegatives+false positives).

The term “immunoassay” includes an assay that utilizes a specificantibody to detect an antigen of interest or utilizes a specific antigento detect an antibody of interest. An immunoassay is thus characterizedby detection of the specific binding of an antigen to an antibody.

The term “sample” or “biological sample” includes a tissue sample or abodily fluid sample. A tissue sample includes, but is not limited to,buccal cells, a brain sample, a skin sample, or an organ sample (e.g.,liver). A bodily fluid sample includes all fluids that are present inthe body including, but not limited to, blood, plasma, serum, saliva,synovial fluid, lymph, urine, or cerebrospinal fluid. The sample mayalso be obtained by subjecting it to a pre-treatment step, if necessary,e.g., by homogenizing the sample or by extracting or isolating acomponent of the sample. Suitable pre-treatment steps may be selected byone skilled in the art depending on nature of the biological sample. Oneskilled in the art will also appreciate that samples such as serumsamples can be diluted prior to analysis.

As used herein, the terms “citrulline” and “citrullinated arginine” areequivalent, and refer to an arginine residue that has been deiminated.As such, it is envisioned that during the preparation of a citrullinatedsynthetic peptide, as provided herein, an arginine residue may beinitially incorporated at a predetermined position in the peptide andsubsequently citrullinated (i.e., deiminated). Alternatively, acitrulline residue may be substituted for the predetermined arginineresidue during peptide synthesis. For the purposes of the presentinvention, when calculating the percent identity of a synthetic peptidewith respect to a reference sequence (i.e., a human protein), acitrulline residue or citrullinated arginine residue is considered to bethe same as an arginine residue found at the equivalent position of thereference sequence. Although citrulline (i.e., deiminated arginine) isstructurally and functionally different than arginine, by definition,for purposes of determining a percent identity only, citrulline isconsidered to be analogous to arginine.

III. Description of the Embodiments

The present invention provides novel citrullinated peptides, their usein methods for aiding, assisting, improving, or facilitating thediagnosis or prognosis of rheumatic diseases such as rheumatoidarthritis (RA), and methods for identifying novel citrullinated peptidesthat are immunoreactive with anti-citrullinated protein antibodies(ACPAs). The present invention also provides methods for detectingrheumatoid factor (RF) using novel RF detection reagents as a means toaid, assist, improve, or facilitate the diagnosis or prognosis ofrheumatic diseases such as RA. Kits comprising at least one of the novelcitrullinated peptides and/or RF detection reagents of the presentinvention are also provided.

In one aspect, the present invention provides a synthetic peptidecomprising a fragment of about 5 to about 50 contiguous amino acids of ahuman protein selected from the group consisting of SEQ ID NOS:1-39,wherein at least one of the contiguous amino acids is an arginineresidue in the native protein, and wherein at least one of the arginineresidues is citrullinated in the synthetic peptide.

In another aspect, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of a human protein selected from the group consisting of SEQ IDNOS:1-39 linked to at least a second fragment of about 5 to about 50contiguous amino acids of a human protein selected from the groupconsisting of SEQ ID NOS:1-39, wherein at least one residue of the firstfragment is an arginine residue in the native protein and at least oneresidue of the second fragment is an arginine residue in the nativeprotein, and wherein at least one of the arginine residues in the firstand/or second fragments is citrullinated in the synthetic peptide. Insome embodiments, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherembodiments, the first and second fragments are linked together by apeptide bond. The first and second fragments of the synthetic peptidemay be derived from the same human protein set forth in SEQ ID NOS:1-39,or may be derived from different proteins.

The synthetic peptide comprising first and second fragments may furtherbe linked to at least a third fragment of about 5 to about 50 contiguousamino acids of a human protein selected from the group consisting of SEQID NOS:1-39, wherein at least one residue of the third fragment is anarginine residue in the native protein. In certain instances, at leastone arginine residue in the third fragment is citrullinated. In someembodiments, the synthetic peptide comprising first, second, and thirdfragments may further be linked to at least a fourth fragment of about 5to about 50 contiguous amino acids of a human protein selected from thegroup consisting of SEQ ID NOS:1-39, wherein at least one residue of thefourth fragment is an arginine residue in the native protein. In certaininstances, at least one arginine residue in the fourth fragment iscitrullinated. In other instances, the first, second, third, and/orfourth fragments are linked together by a peptide bond. In otherembodiments, the synthetic peptide may further comprise at least afifth, sixth, seventh, eighth, ninth, or tenth fragment. Each of thefragments of the synthetic peptide may be derived from the same humanprotein set forth in SEQ ID NOS:1-39, or may be derived from differentproteins.

In yet another aspect, the present invention provides a syntheticpeptide comprising a first synthetic fragment of about 5 to about 50amino acids having homology to a first fragment of about 5 to about 50contiguous amino acids of a human protein selected from the groupconsisting of SEQ ID NOS:1-39 linked to at least a second (andoptionally a third or fourth) synthetic fragment of about 5 to about 50amino acids having homology to a second (and optionally third or fourth)fragment of about 5 to about 50 contiguous amino acids of a humanprotein selected from the group consisting of SEQ ID NOS:1-39, whereinat least one residue of the first synthetic fragment is an arginineresidue in the human protein and at least one residue of the second (andoptionally third or fourth) synthetic fragment is an arginine residue inthe human protein, wherein at least one of the arginine residues iscitrullinated in the synthetic peptide, and wherein the composite aminoacid sequence of the first synthetic fragment and the second (andoptionally third or fourth) synthetic fragment is at least about 80%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or99% identical to the composite amino acid sequence of the first andsecond fragments of the human protein. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth synthetic fragment of about 5 to about 50 aminoacids having homology to a fragment of about 5 to about 50 contiguousamino acids of a human protein selected from the group consisting of SEQID NOS:1-39. Each of the synthetic fragments present in the syntheticpeptide may be derived from the same human protein set forth in SEQ IDNOS:1-39, or may be derived from different proteins.

In one particular embodiment, the present invention provides a syntheticpeptide comprising a fragment of about 5 to about 50 contiguous aminoacids of human vimentin (SEQ ID NO:1), wherein at least one of thecontiguous amino acids is an arginine residue, and wherein at least onearginine residue is citrullinated in the synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 4, 12, 13, 28, 36, 50, 64, 69, 71, 78,100, 122, 158, 159, 207, 217, 222, 270, 310, 320, 321, 364, 401, 410,424, 440, and 450 of SEQ ID NO:1, wherein at least one of the arginineresidues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:1 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:1, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 4, 12, 13, 28, 36, 50, 64, 69, 71, 78, 100, 122, 158, 159,207, 217, 222, 270, 310, 320, 321, 364, 401, 410, 424, 440, and 450 ofSEQ ID NO:1, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:1, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 4, 12, 13, 28, 36, 50, 64, 69, 71, 78, 100, 122, 158, 159,207, 217, 222, 270, 310, 320, 321, 364, 401, 410, 424, 440, and 450 ofSEQ ID NO:1, wherein at least one of the arginine residues in the thirdand/or fourth fragment is citrullinated. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:1, wherein at least one residue of each of thefragments is an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 2-13, 4-12, 22-31, 28-38, 42-52,61-70, 63-78, 68-76, 96-104, 116-124, 158-165, 157-165, 205-217,216-224, 266-276, 320-328, 302-327, 356-364, 393-412, and 417-452 of SEQID NO:1, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:1. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:1. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In particular embodiments, the synthetic peptide of the inventioncomprises a first fragment of amino acids 28-38 of SEQ ID NO:1, linked(e.g., by a peptide bond) to a second fragment of amino acids 42-52 ofSEQ ID NO:1, linked (e.g., by a peptide bond) to a third fragment ofamino acids 61-70 SEQ ID NO:1, wherein at least one of the arginineresidues in each of the fragments is citrullinated (e.g., VMT7 coresequence set forth in SEQ ID NO:53). In alternative embodiments, thesynthetic peptide comprises a first fragment of amino acids 42-52 or61-70 of SEQ ID NO:1, linked (e.g., by a peptide bond) to a secondfragment of amino acids 28-38 or 61-70 of SEQ ID NO:1, linked (e.g., bya peptide bond) to a third fragment of amino acids 28-38 or 42-52 of SEQID NO:1, wherein at least one of the arginine residues in each of thefragments is citrullinated. In other embodiments, the synthetic peptidemay comprise alternative and/or additional fragments of SEQ ID NO:1.

In other particular embodiments, the synthetic peptide of the inventioncomprises a first fragment of amino acids 63-78 of SEQ ID NO:1, linked(e.g., by a peptide bond) to a second fragment of amino acids 68-76 ofSEQ ID NO:1, wherein at least one of the arginine residues in each ofthe fragments is citrullinated (e.g., VMT8 core sequence set forth inSEQ ID NO:55). In alternative embodiments, the synthetic peptidecomprises a first fragment of amino acids 68-76 of SEQ ID NO:1, linked(e.g., by a peptide bond) to a second fragment of amino acids 63-78 ofSEQ ID NO:1, wherein at least one of the arginine residues in each ofthe fragments is citrullinated. In other embodiments, the syntheticpeptide may comprise alternative and/or additional fragments of SEQ IDNO:1.

In further particular embodiments, the synthetic peptide of theinvention comprises a first fragment of amino acids 356-364 of SEQ IDNO:1, linked (e.g., by a peptide bond) to a second fragment of aminoacids 393-412 of SEQ ID NO:1, wherein at least one of the arginineresidues in each of the fragments is citrullinated (e.g., VMT13 coresequence set forth in SEQ ID NO:65). In alternative embodiments, thesynthetic peptide comprises a first fragment of amino acids 393-412 ofSEQ ID NO:1, linked (e.g., by a peptide bond) to a second fragment ofamino acids 356-364 of SEQ ID NO:1, wherein at least one of the arginineresidues in each of the fragments is citrullinated. In otherembodiments, the synthetic peptide may comprise alternative and/oradditional fragments of SEQ ID NO:1.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:1 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human fibrinogen alpha-chain (SEQ ID NO:2),wherein at least one of the contiguous amino acids is an arginineresidue, and wherein at least one arginine residue is citrullinated inthe synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 38, 42, 84, 114, 129, 135, 143, 160, 178,181, 186, 216, 218, 367, 394, 458, 459, 512, 547, 591, 621, 627, and 630of SEQ ID NO:2, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:2 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:2, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 38, 42, 84, 114, 129, 135, 143, 160, 178, 181, 186, 216, 218,367, 394, 458, 459, 512, 547, 591, 621, 627, and 630 of SEQ ID NO:2,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:2, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 38, 42, 84, 114, 129, 135, 143, 160, 178, 181, 186, 216, 218,367, 394, 458, 459, 512, 547, 591, 621, 627, and 630 of SEQ ID NO:2,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:2, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 35-43, 76-89, 107-136, 127-148,153-161, 174-188, 177-183, 212-220, 213-220, 359-368, 393-401, 440-450,451-465, 509-517, 539-549, 583-599, and 613-639 of SEQ ID NO:2, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:2. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:2. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:2 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human fibrinogen beta-chain (SEQ ID NO:3),wherein at least one of the contiguous amino acids is an arginineresidue, and wherein at least one arginine residue is citrullinated inthe synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 47, 53, 60, 72, 74, 158, 196, 199, 206,224, 334, 376, and 421 of SEQ ID NO:3, wherein at least one of thearginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:3 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:3, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 47, 53, 60, 72, 74, 158, 196, 199, 206, 224, 334, 376, and 421of SEQ ID NO:3, wherein at least one of the arginine residues in thefirst fragment is citrullinated, and wherein at least one of thearginine residues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:3, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 47, 53, 60, 72, 74, 158, 196, 199, 206, 224, 334, 376, and 421of SEQ ID NO:3, wherein at least one of the arginine residues in thethird and/or fourth fragment is citrullinated. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:3, wherein at least one residue of each of thefragments is an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 70-79, 150-158, 188-200,192-204, 198-207, 220-230, 327-336, 368-376, and 415-423 of SEQ ID NO:3,wherein the fragments are linked together (e.g., by a peptide bond), andwherein at least one of the arginine residues in each of the fragmentsis citrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:3. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:3. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:3 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human fibrinogen gamma-chain (SEQ ID NO:4),wherein at least one of the contiguous amino acids is an arginineresidue, and wherein at least one arginine residue is citrullinated inthe synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 31, 40, 134, 223, 301, and 417 of SEQ IDNO:4, wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:4 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:4, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 31, 40, 134, 223, 301, and 417 of SEQ ID NO:4, wherein atleast one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:4, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 31, 40, 134, 223, 301, and 417 of SEQ ID NO:4, wherein atleast one of the arginine residues in the third and/or fourth fragmentis citrullinated. In other embodiments, the synthetic peptide mayfurther comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:4, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 27-43, 126-135, 219-230,300-308, and 409-419 of SEQ ID NO:4, wherein the fragments are linkedtogether (e.g., by a peptide bond), and wherein at least one of thearginine residues in each of the fragments is citrullinated. Thesynthetic peptides of the invention having a composite amino acidsequence may comprise at least two, three, four, five, six, seven,eight, nine, ten, or more independently selected fragments of SEQ IDNO:4. In some embodiments, the synthetic peptide comprises one, two, orthree independently selected fragments of SEQ ID NO:4. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:4 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human alpha-enolase (SEQ ID NO:5), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 9, 15, 32, 50, 132, 269, 327, 372, 412,and 429 of SEQ ID NO:5, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:5 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:5, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 9, 15, 32, 50, 132, 269, 327, 372, 412, and 429 of SEQ IDNO:5, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:5, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 9, 15, 32, 50, 132, 269, 327, 372, 412, and 429 of SEQ IDNO:5, wherein at least one of the arginine residues in the third and/orfourth fragment is citrullinated. In other embodiments, the syntheticpeptide may further comprise at least a fifth, sixth, seventh, eighth,ninth, or tenth fragment of about 5 to about 50 contiguous amino acidsof SEQ ID NO:5, wherein at least one residue of each of the fragments isan arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 12-22, 29-40, 47-56, 130-139,268-279, 321-330, 364-376, 411-419, and 425-434 of SEQ ID NO:5, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:5. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:5. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:5 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human fibronectin 1 (SEQ ID NO:6), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 222, 228, 230, 237, 241, 1016, 1021,1028, 1035, 1197, 1207, 1382, 1389, 1391, 1402, 1405, 1410, 1524, 1539,1661, 1663, 1821, 1835, 1859, 1866, 2058, and 2059 of SEQ ID NO:6,wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:6 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:6, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 222, 228, 230, 237, 241, 1016, 1021, 1028, 1035, 1197, 1207,1382, 1389, 1391, 1402, 1405, 1410, 1524, 1539, 1661, 1663, 1821, 1835,1859, 1866, 2058, and 2059 of SEQ ID NO:6, wherein at least one of thearginine residues in the first fragment is citrullinated, and wherein atleast one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:6, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 222, 228, 230, 237, 241, 1016, 1021, 1028, 1035, 1197, 1207,1382, 1389, 1391, 1402, 1405, 1410, 1524, 1539, 1661, 1663, 1821, 1835,1859, 1866, 2058, and 2059 of SEQ ID NO:6, wherein at least one of thearginine residues in the third and/or fourth fragment is citrullinated.In other embodiments, the synthetic peptide may further comprise atleast a fifth, sixth, seventh, eighth, ninth, or tenth fragment of about5 to about 50 contiguous amino acids of SEQ ID NO:6, wherein at leastone residue of each of the fragments is an arginine residue in thenative protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 215-229, 221-229, 221-230,231-239, 233-241, 1013-1021, 1014-1023, 1020-1035, 1027-1035, 1189-1214,1379-1387, 1381-1389, 1388-1396, 1401-1409, 1401-1417, 1517-1546,1655-1668, 1818-1837, 1851-1872, 2056-2065, and 2057-2066 of SEQ IDNO:6, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:6. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:6. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:6 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human lamin B1 (SEQ ID NO:7), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 208, 220, 226, 234, 397, 402, 407, 410,413, 416, 542, and 577 of SEQ ID NO:7, wherein at least one of thearginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:7 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:7, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 208, 220, 226, 234, 397, 402, 407, 410, 413, 416, 542, and 577of SEQ ID NO:7, wherein at least one of the arginine residues in thefirst fragment is citrullinated, and wherein at least one of thearginine residues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:7, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 208, 220, 226, 234, 397, 402, 407, 410, 413, 416, 542, and 577of SEQ ID NO:7, wherein at least one of the arginine residues in thethird and/or fourth fragment is citrullinated. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:7, wherein at least one residue of each of thefragments is an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 205-229, 220-235, 395-409,395-415, 406-425, 533-548, and 570-582 of SEQ ID NO:7, wherein thefragments are linked together (e.g., by a peptide bond), and wherein atleast one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:7. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:7. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:7 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human lamin B2 (SEQ ID NO:8), wherein at leastone of the contiguous amino acids is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 185, 191, 219, 220, 228, 391, 396, 555,564, and 591 of SEQ ID NO:8, wherein at least one of the arginineresidues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:8 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:8, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 185, 191, 219, 220, 228, 391, 396, 555, 564, and 591 of SEQ IDNO:8, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:8, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 185, 191, 219, 220, 228, 391, 396, 555, 564, and 591 of SEQ IDNO:8, wherein at least one of the arginine residues in the third and/orfourth fragment is citrullinated. In other embodiments, the syntheticpeptide may further comprise at least a fifth, sixth, seventh, eighth,ninth, or tenth fragment of about 5 to about 50 contiguous amino acidsof SEQ ID NO:8, wherein at least one residue of each of the fragments isan arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 178-192, 184-193, 218-227,219-231, 383-392, 389-404, 550-569, and 584-595 of SEQ ID NO:8, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:8. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:8. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:8 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human lamin A/C (SEQ ID NO:9), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 7, 8, 11, 48, 50, 62, 72, 220, 221, 225,235, 288, 296, 298, 399, 401, 419, 427, 435, 541, 545, 582, 584, 624,627, 644, and 654 of SEQ ID NO:9, wherein at least one of the arginineresidues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:9 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:9, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 7, 8, 11, 48, 50, 62, 72, 220, 221, 225, 235, 288, 296, 298,399, 401, 419, 427, 435, 541, 545, 582, 584, 624, 627, 644, and 654 ofSEQ ID NO:9, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:9, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 7, 8, 11, 48, 50, 62, 72, 220, 221, 225, 235, 288, 296, 298,399, 401, 419, 427, 435, 541, 545, 582, 584, 624, 627, 644, and 654 ofSEQ ID NO:9, wherein at least one of the arginine residues in the thirdand/or fourth fragment is citrullinated. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:9, wherein at least one residue of each of thefragments is an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 5-13, 7-15, 7-16, 43-52, 43-58,58-78, 218-227, 219-227, 219-236, 294-305, 296-305, 284-296, 399-407,410-428, 418-441, 537-549, 541-552, 574-588, 580-590, 617-629, 619-628,and 636-657 of SEQ ID NO:9, wherein the fragments are linked together(e.g., by a peptide bond), and wherein at least one of the arginineresidues in each of the fragments is citrullinated. The syntheticpeptides of the invention having a composite amino acid sequence maycomprise at least two, three, four, five, six, seven, eight, nine, ten,or more independently selected fragments of SEQ ID NO:9. In someembodiments, the synthetic peptide comprises one, two, or threeindependently selected fragments of SEQ ID NO:9. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:9 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human (3-actin (SEQ ID NO:10), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 196 and 206 of SEQ ID NO:10, wherein atleast one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:10 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:10, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 196 and 206 of SEQ ID NO:10, wherein at least one of thearginine residues in the first fragment is citrullinated, and wherein atleast one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:10, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 196 and 206 of SEQ ID NO:10, wherein at least one of thearginine residues in the third and/or fourth fragment is citrullinated.In other embodiments, the synthetic peptide may further comprise atleast a fifth, sixth, seventh, eighth, ninth, or tenth fragment of about5 to about 50 contiguous amino acids of SEQ ID NO:10, wherein at leastone residue of each of the fragments is an arginine residue in thenative protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 188-207 of SEQ ID NO:10, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:10. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:10. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:10 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human myeloblastin (SEQ ID NO:11), whereinat least one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 39, 48, 79, 91, 227, 235, 244, 248, and249 of SEQ ID NO:11, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:11 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:11, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 39, 48, 79, 91, 227, 235, 244, 248, and 249 of SEQ ID NO:11,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:11, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 39, 48, 79, 91, 227, 235, 244, 248, and 249 of SEQ ID NO:11,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:11, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 37-54, 71-99, 218-241, 241-249,241-250, and 242-251 of SEQ ID NO:11, wherein the fragments are linkedtogether (e.g., by a peptide bond), and wherein at least one of thearginine residues in each of the fragments is citrullinated. Thesynthetic peptides of the invention having a composite amino acidsequence may comprise at least two, three, four, five, six, seven,eight, nine, ten, or more independently selected fragments of SEQ IDNO:11. In some embodiments, the synthetic peptide comprises one, two, orthree independently selected fragments of SEQ ID NO:11. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:11 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human PL scramblase (SEQ ID NO:12), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 163, 177, and 180 of SEQ ID NO:12,wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:12 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:12, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 163, 177, and 180 of SEQ ID NO:12, wherein at least one of thearginine residues in the first fragment is citrullinated, and wherein atleast one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:12, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 163, 177, and 180 of SEQ ID NO:12, wherein at least one of thearginine residues in the third and/or fourth fragment is citrullinated.In other embodiments, the synthetic peptide may further comprise atleast a fifth, sixth, seventh, eighth, ninth, or tenth fragment of about5 to about 50 contiguous amino acids of SEQ ID NO:12, wherein at leastone residue of each of the fragments is an arginine residue in thenative protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 161-181 and 173-182 of SEQ IDNO:12, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:12. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:12. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:12 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human apolipoprotein (a) (SEQ ID NO:13),wherein at least one of the contiguous amino acids is an arginineresidue, and wherein at least one arginine residue is citrullinated inthe synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 37, 47, 91, 96, 136, 3571, 3695, 3710,3722, 3726, 3905, 3915, 3930, 3942, 3946, 4019, 4029, 4133, 4143, 4155,4158, 4533, and 4536 of SEQ ID NO:13, wherein at least one of thearginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:13 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:13, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 37, 47, 91, 96, 136, 3571, 3695, 3710, 3722, 3726, 3905, 3915,3930, 3942, 3946, 4019, 4029, 4133, 4143, 4155, 4158, 4533, and 4536 ofSEQ ID NO:13, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:13, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 37, 47, 91, 96, 136, 3571, 3695, 3710, 3722, 3726, 3905, 3915,3930, 3942, 3946, 4019, 4029, 4133, 4143, 4155, 4158, 4533, and 4536 ofSEQ ID NO:13, wherein at least one of the arginine residues in the thirdand/or fourth fragment is citrullinated. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:13, wherein at least one residue of each of thefragments is an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 29-51, 89-97, 128-136,3563-3572, 3687-3699, 3706-3722, 3718-3727, 3897-3919, 3926-3942,3938-3947, 4011-4033, 4131-4156, 4155-4162, 4529-4541, and 4530-4539 ofSEQ ID NO:13, wherein the fragments are linked together (e.g., by apeptide bond), and wherein at least one of the arginine residues in eachof the fragments is citrullinated. The synthetic peptides of theinvention having a composite amino acid sequence may comprise at leasttwo, three, four, five, six, seven, eight, nine, ten, or moreindependently selected fragments of SEQ ID NO:13. In some embodiments,the synthetic peptide comprises one, two, or three independentlyselected fragments of SEQ ID NO:13. Preferably, the fragments are linkedtogether by peptide bonds, e.g., a first fragment is linked to a secondfragment by a peptide bond, which is linked to a third fragment by apeptide bond, with the resulting synthetic peptide having a linearstructure. The fragments of the synthetic peptide may be linked togetherin any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:13 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human BiP (SEQ ID NO:14), wherein at leastone of the contiguous amino acids is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 181, 197, 283, 290, 297, 324, 336, 367,439, and 532 of SEQ ID NO:14, wherein at least one of the arginineresidues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:14 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:14, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 181, 197, 283, 290, 297, 324, 336, 367, 439, and 532 of SEQ IDNO:14, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:14, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 181, 197, 283, 290, 297, 324, 336, 367, 439, and 532 of SEQ IDNO:14, wherein at least one of the arginine residues in the third and/orfourth fragment is citrullinated. In other embodiments, the syntheticpeptide may further comprise at least a fifth, sixth, seventh, eighth,ninth, or tenth fragment of about 5 to about 50 contiguous amino acidsof SEQ ID NO:14, wherein at least one residue of each of the fragmentsis an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 175-183, 190-203, 277-304,315-324, 333-341, 359-367, 435-444, and 524-534 of SEQ ID NO:14, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:14. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:14. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:14 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human histone H2A (SEQ ID NO:15), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 72 and 82 of SEQ ID NO:15, wherein atleast one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:15 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:15, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 72 and 82 of SEQ ID NO:15, wherein at least one of thearginine residues in the first fragment is citrullinated, and wherein atleast one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:15, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 72 and 82 of SEQ ID NO:15, wherein at least one of thearginine residues in the third and/or fourth fragment is citrullinated.In other embodiments, the synthetic peptide may further comprise atleast a fifth, sixth, seventh, eighth, ninth, or tenth fragment of about5 to about 50 contiguous amino acids of SEQ ID NO:15, wherein at leastone residue of each of the fragments is an arginine residue in thenative protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 64-85 of SEQ ID NO:15, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:15. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:15. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:15 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human histone H₂B (SEQ ID NO:16), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 34, 73, 80, 87, 93, and 100 of SEQ IDNO:16, wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:16 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:16, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 34, 73, 80, 87, 93, and 100 of SEQ ID NO:16, wherein at leastone of the arginine residues in the first fragment is citrullinated, andwherein at least one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:16, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 34, 73, 80, 87, 93, and 100 of SEQ ID NO:16, wherein at leastone of the arginine residues in the third and/or fourth fragment iscitrullinated. In other embodiments, the synthetic peptide may furthercomprise at least a fifth, sixth, seventh, eighth, ninth, or tenthfragment of about 5 to about 50 contiguous amino acids of SEQ ID NO:16,wherein at least one residue of each of the fragments is an arginineresidue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 31-44, 65-94, and 79-101 of SEQID NO:16, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:16. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:16. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:16 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human histone H3 (SEQ ID NO:17), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 24, 50, 53, 64, 84, and 135 of SEQ IDNO:17, wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:17 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:17, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 24, 50, 53, 64, 84, and 135 of SEQ ID NO:17, wherein at leastone of the arginine residues in the first fragment is citrullinated, andwherein at least one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:17, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 24, 50, 53, 64, 84, and 135 of SEQ ID NO:17, wherein at leastone of the arginine residues in the third and/or fourth fragment iscitrullinated. In other embodiments, the synthetic peptide may furthercomprise at least a fifth, sixth, seventh, eighth, ninth, or tenthfragment of about 5 to about 50 contiguous amino acids of SEQ ID NO:17,wherein at least one residue of each of the fragments is an arginineresidue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 41-70, 78-91, and 128-136 of SEQID NO:17, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:17. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:17. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:17 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In a further particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human histone H4 (SEQ ID NO:21), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 24, 56, 68, 79, and 96 of SEQ ID NO:21,wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:21 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:21, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 24, 56, 68, 79, and 96 of SEQ ID NO:21, wherein at least oneof the arginine residues in the first fragment is citrullinated, andwherein at least one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:21, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 24, 56, 68, 79, and 96 of SEQ ID NO:21, wherein at least oneof the arginine residues in the third and/or fourth fragment iscitrullinated. In other embodiments, the synthetic peptide may furthercomprise at least a fifth, sixth, seventh, eighth, ninth, or tenthfragment of about 5 to about 50 contiguous amino acids of SEQ ID NO:21,wherein at least one residue of each of the fragments is an arginineresidue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 20-29, 49-84, and 92-100 of SEQID NO:21, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:21. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:21. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:21 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human collagen T2α1 (SEQ ID NO:22), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 1270, 1379, 1422, 1428, 1453, and 1459 ofSEQ ID NO:22, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:22 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:22, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 1270, 1379, 1422, 1428, 1453, and 1459 of SEQ ID NO:22,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:22, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 1270, 1379, 1422, 1428, 1453, and 1459 of SEQ ID NO:22,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:22, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 1263-1271, 1371-1386, 1420-1429,1421-1436, 1444-1460, and 1452-1460 of SEQ ID NO:22, wherein thefragments are linked together (e.g., by a peptide bond), and wherein atleast one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:22. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:22. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:22 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human collagen T9α1 (SEQ ID NO:23), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 30, 71, 76, 100, 118, 189, 200, 768, and783 of SEQ ID NO:23, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:23 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:23, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 30, 71, 76, 100, 118, 189, 200, 768, and 783 of SEQ ID NO:23,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:23, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 30, 71, 76, 100, 118, 189, 200, 768, and 783 of SEQ ID NO:23,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:23, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 26-35, 63-71, 72-81, 73-80,96-104, 111-126, 181-207, and 760-783 of SEQ ID NO:23, wherein thefragments are linked together (e.g., by a peptide bond), and wherein atleast one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:23. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:23. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:23 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human collagen T10α1 (SEQ ID NO:24),wherein at least one of the contiguous amino acids is an arginineresidue, and wherein at least one arginine residue is citrullinated inthe synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 531, 578, and 585 of SEQ ID NO:24,wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:24 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:24, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 531, 578, and 585 of SEQ ID NO:24, wherein at least one of thearginine residues in the first fragment is citrullinated, and wherein atleast one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:24, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 531, 578, and 585 of SEQ ID NO:24, wherein at least one of thearginine residues in the third and/or fourth fragment is citrullinated.In other embodiments, the synthetic peptide may further comprise atleast a fifth, sixth, seventh, eighth, ninth, or tenth fragment of about5 to about 50 contiguous amino acids of SEQ ID NO:24, wherein at leastone residue of each of the fragments is an arginine residue in thenative protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 527-536, 572-580, and 585-593 ofSEQ ID NO:24, wherein the fragments are linked together (e.g., by apeptide bond), and wherein at least one of the arginine residues in eachof the fragments is citrullinated. The synthetic peptides of theinvention having a composite amino acid sequence may comprise at leasttwo, three, four, five, six, seven, eight, nine, ten, or moreindependently selected fragments of SEQ ID NO:24. In some embodiments,the synthetic peptide comprises one, two, or three independentlyselected fragments of SEQ ID NO:24. Preferably, the fragments are linkedtogether by peptide bonds, e.g., a first fragment is linked to a secondfragment by a peptide bond, which is linked to a third fragment by apeptide bond, with the resulting synthetic peptide having a linearstructure. The fragments of the synthetic peptide may be linked togetherin any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:24 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human collagen T11α1 (SEQ ID NO:25), whereinat least one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 64, 75, 155, 166, 192, 195, and 1555 ofSEQ ID NO:25, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:25 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:25, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 64, 75, 155, 166, 192, 195, and 1555 of SEQ ID NO:25, whereinat least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:25, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 64, 75, 155, 166, 192, 195, and 1555 of SEQ ID NO:25, whereinat least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:25, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 61-83, 150-174, 187-196,188-196, and 1555-1564 of SEQ ID NO:25, wherein the fragments are linkedtogether (e.g., by a peptide bond), and wherein at least one of thearginine residues in each of the fragments is citrullinated. Thesynthetic peptides of the invention having a composite amino acidsequence may comprise at least two, three, four, five, six, seven,eight, nine, ten, or more independently selected fragments of SEQ IDNO:25. In some embodiments, the synthetic peptide comprises one, two, orthree independently selected fragments of SEQ ID NO:25. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:25 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human collagen T11α2 (SEQ ID NO:27), whereinat least one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 61, 64, 73, 91, 93, 243, 246, 254, and257 of SEQ ID NO:27, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:27 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:27, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 61, 64, 73, 91, 93, 243, 246, 254, and 257 of SEQ ID NO:27,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:27, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 61, 64, 73, 91, 93, 243, 246, 254, and 257 of SEQ ID NO:27,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:27, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 52-68, 60-74, 82-92, 85-98,238-262, and 242-262 of SEQ ID NO:27, wherein the fragments are linkedtogether (e.g., by a peptide bond), and wherein at least one of thearginine residues in each of the fragments is citrullinated. Thesynthetic peptides of the invention having a composite amino acidsequence may comprise at least two, three, four, five, six, seven,eight, nine, ten, or more independently selected fragments of SEQ IDNO:27. In some embodiments, the synthetic peptide comprises one, two, orthree independently selected fragments of SEQ ID NO:27. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:27 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human syndecan-I (SEQ ID NO:28), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 126, 190, 229, and 230 of SEQ ID NO:28,wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:28 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:28, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 126, 190, 229, and 230 of SEQ ID NO:28, wherein at least oneof the arginine residues in the first fragment is citrullinated, andwherein at least one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:28, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 126, 190, 229, and 230 of SEQ ID NO:28, wherein at least oneof the arginine residues in the third and/or fourth fragment iscitrullinated. In other embodiments, the synthetic peptide may furthercomprise at least a fifth, sixth, seventh, eighth, ninth, or tenthfragment of about 5 to about 50 contiguous amino acids of SEQ ID NO:28,wherein at least one residue of each of the fragments is an arginineresidue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 123-131, 183-191, 225-238, and229-238 of SEQ ID NO:28, wherein the fragments are linked together(e.g., by a peptide bond), and wherein at least one of the arginineresidues in each of the fragments is citrullinated. The syntheticpeptides of the invention having a composite amino acid sequence maycomprise at least two, three, four, five, six, seven, eight, nine, ten,or more independently selected fragments of SEQ ID NO:28. In someembodiments, the synthetic peptide comprises one, two, or threeindependently selected fragments of SEQ ID NO:28. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:28 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In a further particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human syndecan-III (SEQ ID NO:29), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 98, 155, 204, 209, 210, 223, 247, 255,261, and 273 of SEQ ID NO:29, wherein at least one of the arginineresidues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:29 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:29, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 98, 155, 204, 209, 210, 223, 247, 255, 261, and 273 of SEQ IDNO:29, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:29, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 98, 155, 204, 209, 210, 223, 247, 255, 261, and 273 of SEQ IDNO:29, wherein at least one of the arginine residues in the third and/orfourth fragment is citrullinated. In other embodiments, the syntheticpeptide may further comprise at least a fifth, sixth, seventh, eighth,ninth, or tenth fragment of about 5 to about 50 contiguous amino acidsof SEQ ID NO:29, wherein at least one residue of each of the fragmentsis an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 91-99, 147-161, 196-209,201-211, 202-211, 222-224, and 246-274 of SEQ ID NO:29, wherein thefragments are linked together (e.g., by a peptide bond), and wherein atleast one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:29. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:29. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:29 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human CD44 (SEQ ID NO:30), wherein at leastone of the contiguous amino acids is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 29, 41, 46, 78, 90, 150, 154, 186, 218,313, 343, 349, 417, 440, 469, 470, 537, 544, 545, 600, and 643 of SEQ IDNO:30, wherein at least one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:30 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:30, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 29, 41, 46, 78, 90, 150, 154, 186, 218, 313, 343, 349, 417,440, 469, 470, 537, 544, 545, 600, and 643 of SEQ ID NO:30, wherein atleast one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:30, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 29, 41, 46, 78, 90, 150, 154, 186, 218, 313, 343, 349, 417,440, 469, 470, 537, 544, 545, 600, and 643 of SEQ ID NO:30, wherein atleast one of the arginine residues in the third and/or fourth fragmentis citrullinated. In other embodiments, the synthetic peptide mayfurther comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:30, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 22-42, 40-50, 72-97, 142-156,149-156, 179-187, 211-226, 306-314, 335-345, 343-350, 411-420, 437-445,469-477, 530-538, 537-544, 543-551, 593-604, and 641-647 of SEQ IDNO:30, wherein the fragments are linked together (e.g., by a peptidebond), and wherein at least one of the arginine residues in each of thefragments is citrullinated. The synthetic peptides of the inventionhaving a composite amino acid sequence may comprise at least two, three,four, five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:30. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:30. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:30 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human ICAM-I (SEQ ID NO:31), wherein at leastone of the contiguous amino acids is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 143, 152, 159, 176, 187, 193, 460, 468,and 478 of SEQ ID NO:31, wherein at least one of the arginine residuesis citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:31 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:31, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 143, 152, 159, 176, 187, 193, 460, 468, and 478 of SEQ IDNO:31, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:31, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 143, 152, 159, 176, 187, 193, 460, 468, and 478 of SEQ IDNO:31, wherein at least one of the arginine residues in the third and/orfourth fragment is citrullinated. In other embodiments, the syntheticpeptide may further comprise at least a fifth, sixth, seventh, eighth,ninth, or tenth fragment of about 5 to about 50 contiguous amino acidsof SEQ ID NO:31, wherein at least one residue of each of the fragmentsis an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 140-152, 151-159, 168-179,181-188, 186-194, and 456-480 of SEQ ID NO:31, wherein the fragments arelinked together (e.g., by a peptide bond), and wherein at least one ofthe arginine residues in each of the fragments is citrullinated. Thesynthetic peptides of the invention having a composite amino acidsequence may comprise at least two, three, four, five, six, seven,eight, nine, ten, or more independently selected fragments of SEQ IDNO:31. In some embodiments, the synthetic peptide comprises one, two, orthree independently selected fragments of SEQ ID NO:31. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:31 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human VCAM-I (SEQ ID NO:32), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 499 and 512 of SEQ ID NO:32, wherein atleast one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:32 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:32, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 499 and 512 of SEQ ID NO:32, wherein at least one of thearginine residues in the first fragment is citrullinated, and wherein atleast one of the arginine residues in the second fragment iscitrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:32, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 499 and 512 of SEQ ID NO:32, wherein at least one of thearginine residues in the third and/or fourth fragment is citrullinated.In other embodiments, the synthetic peptide may further comprise atleast a fifth, sixth, seventh, eighth, ninth, or tenth fragment of about5 to about 50 contiguous amino acids of SEQ ID NO:32, wherein at leastone residue of each of the fragments is an arginine residue in thenative protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 496-520 of SEQ ID NO:32, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:32. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:32. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:32 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human glypican-I (SEQ ID NO:33), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 90, 94, 105, 139, 142, 149, 153, 212,215, 221, 235, 248, 466, 468, 505, and 511 of SEQ ID NO:33, wherein atleast one of the arginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:33 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:33, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 90, 94, 105, 139, 142, 149, 153, 212, 215, 221, 235, 248, 466,468, 505, and 511 of SEQ ID NO:33, wherein at least one of the arginineresidues in the first fragment is citrullinated, and wherein at leastone of the arginine residues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:33, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 90, 94, 105, 139, 142, 149, 153, 212, 215, 221, 235, 248, 466,468, 505, and 511 of SEQ ID NO:33, wherein at least one of the arginineresidues in the third and/or fourth fragment is citrullinated. In otherembodiments, the synthetic peptide may further comprise at least afifth, sixth, seventh, eighth, ninth, or tenth fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:33, wherein at least oneresidue of each of the fragments is an arginine residue in the nativeprotein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 87-95, 88-106, 131-140, 139-146,141-158, 209-225, 211-219, 227-250, 459-469, 460-473, 499-512, and504-512 of SEQ ID NO:33, wherein the fragments are linked together(e.g., by a peptide bond), and wherein at least one of the arginineresidues in each of the fragments is citrullinated. The syntheticpeptides of the invention having a composite amino acid sequence maycomprise at least two, three, four, five, six, seven, eight, nine, ten,or more independently selected fragments of SEQ ID NO:33. In someembodiments, the synthetic peptide comprises one, two, or threeindependently selected fragments of SEQ ID NO:33. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:33 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human glypican-II (SEQ ID NO:34), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 76, 79, 86, 214, 219, 225, 281, 287, 355,357, 358, 469, 471, and 480 of SEQ ID NO:34, wherein at least one of thearginine residues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:34 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:34, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 76, 79, 86, 214, 219, 225, 281, 287, 355, 357, 358, 469, 471,and 480 of SEQ ID NO:34, wherein at least one of the arginine residuesin the first fragment is citrullinated, and wherein at least one of thearginine residues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:34, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 76, 79, 86, 214, 219, 225, 281, 287, 355, 357, 358, 469, 471,and 480 of SEQ ID NO:34, wherein at least one of the arginine residuesin the third and/or fourth fragment is citrullinated. In otherembodiments, the synthetic peptide may further comprise at least afifth, sixth, seventh, eighth, ninth, or tenth fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:34, wherein at least oneresidue of each of the fragments is an arginine residue in the nativeprotein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 68-76, 76-87, 212-229, 213-223,273-288, 283-288, 351-359, 461-470, and 470-482 of SEQ ID NO:34, whereinthe fragments are linked together (e.g., by a peptide bond), and whereinat least one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:34. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:34. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:34 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In still yet another particular embodiment, the present inventionprovides a synthetic peptide comprising a fragment of about 5 to about50 contiguous amino acids of human glypican-IV (SEQ ID NO:35), whereinat least one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 167, 174, 213, 219, 351, 354, 463, and469 of SEQ ID NO:35, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:35 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:35, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 167, 174, 213, 219, 351, 354, 463, and 469 of SEQ ID NO:35,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:35, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 167, 174, 213, 219, 351, 354, 463, and 469 of SEQ ID NO:35,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:35, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 160-181, 207-216, 212-223,350-358, 350-362, 462-470, and 465-476 of SEQ ID NO:35, wherein thefragments are linked together (e.g., by a peptide bond), and wherein atleast one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:35. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:35. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:35 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human glypican-V (SEQ ID NO:36), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 76, 82, 198, 199, 210, 343, 347, 350,357, 392, and 395 of SEQ ID NO:36, wherein at least one of the arginineresidues is citrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:36 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:36, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 76, 82, 198, 199, 210, 343, 347, 350, 357, 392, and 395 of SEQID NO:36, wherein at least one of the arginine residues in the firstfragment is citrullinated, and wherein at least one of the arginineresidues in the second fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:36, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 76, 82, 198, 199, 210, 343, 347, 350, 357, 392, and 395 of SEQID NO:36, wherein at least one of the arginine residues in the thirdand/or fourth fragment is citrullinated. In other embodiments, thesynthetic peptide may further comprise at least a fifth, sixth, seventh,eighth, ninth, or tenth fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:36, wherein at least one residue of each of thefragments is an arginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 70-83, 75-87, 194-205, 197-214,336-354, 346-358, 385-399, and 387-399 of SEQ ID NO:36, wherein thefragments are linked together (e.g., by a peptide bond), and wherein atleast one of the arginine residues in each of the fragments iscitrullinated. The synthetic peptides of the invention having acomposite amino acid sequence may comprise at least two, three, four,five, six, seven, eight, nine, ten, or more independently selectedfragments of SEQ ID NO:36. In some embodiments, the synthetic peptidecomprises one, two, or three independently selected fragments of SEQ IDNO:36. Preferably, the fragments are linked together by peptide bonds,e.g., a first fragment is linked to a second fragment by a peptide bond,which is linked to a third fragment by a peptide bond, with theresulting synthetic peptide having a linear structure. The fragments ofthe synthetic peptide may be linked together in any order ororientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:36 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In yet another particular embodiment, the present invention provides asynthetic peptide comprising a fragment of about 5 to about 50contiguous amino acids of human glypican-VI (SEQ ID NO:37), wherein atleast one of the contiguous amino acids is an arginine residue, andwherein at least one arginine residue is citrullinated in the syntheticpeptide.

In certain embodiments, the fragment comprises at least one of thearginine residues at positions 95, 101, 213, 219, 229, 234, 461, and 468of SEQ ID NO:37, wherein at least one of the arginine residues iscitrullinated.

In other embodiments, the present invention provides a synthetic peptidecomprising a first fragment of about 5 to about 50 contiguous aminoacids of SEQ ID NO:37 linked to at least a second fragment of about 5 toabout 50 contiguous amino acids of SEQ ID NO:37, wherein at least oneresidue of the first fragment is an arginine residue and at least oneresidue of the second fragment is an arginine residue, and wherein atleast one arginine residue is citrullinated in the synthetic peptide.

In some instances, the first and second fragments of the syntheticpeptide each comprise at least one citrullinated arginine. In otherinstances, the first and second fragments are linked together by apeptide bond. In further instances, the first and second fragmentsindependently comprise at least one of the arginine residues atpositions 95, 101, 213, 219, 229, 234, 461, and 468 of SEQ ID NO:37,wherein at least one of the arginine residues in the first fragment iscitrullinated, and wherein at least one of the arginine residues in thesecond fragment is citrullinated.

The synthetic peptide comprising first and second fragments may furthercomprise at least a third or fourth fragment of about 5 to about 50contiguous amino acids of SEQ ID NO:37, wherein at least one residue ofeach of the third or fourth fragments is an arginine residue in thenative protein. In certain instances, at least one arginine residue inthe third and/or fourth fragment is citrullinated. In other instances,the first, second, third, and/or fourth fragments are linked together bya peptide bond. In further instances, the third and fourth fragmentsindependently comprise at least one of the arginine residues atpositions 95, 101, 213, 219, 229, 234, 461, and 468 of SEQ ID NO:37,wherein at least one of the arginine residues in the third and/or fourthfragment is citrullinated. In other embodiments, the synthetic peptidemay further comprise at least a fifth, sixth, seventh, eighth, ninth, ortenth fragment of about 5 to about 50 contiguous amino acids of SEQ IDNO:37, wherein at least one residue of each of the fragments is anarginine residue in the native protein.

In certain other embodiments, the present invention provides a syntheticpeptide comprising one or more fragments independently selected from thegroup consisting of amino acid residues 91-102, 93-102, 206-234,226-241, 454-462, and 460-475 of SEQ ID NO:37, wherein the fragments arelinked together (e.g., by a peptide bond), and wherein at least one ofthe arginine residues in each of the fragments is citrullinated. Thesynthetic peptides of the invention having a composite amino acidsequence may comprise at least two, three, four, five, six, seven,eight, nine, ten, or more independently selected fragments of SEQ IDNO:37. In some embodiments, the synthetic peptide comprises one, two, orthree independently selected fragments of SEQ ID NO:37. Preferably, thefragments are linked together by peptide bonds, e.g., a first fragmentis linked to a second fragment by a peptide bond, which is linked to athird fragment by a peptide bond, with the resulting synthetic peptidehaving a linear structure. The fragments of the synthetic peptide may belinked together in any order or orientation.

In certain instances, the synthetic peptide comprising one or morefragments of SEQ ID NO:37 is about 5-50, 8-50, 8-25, 8-15, 10-50, 10-45,10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45, 15-40, 15-35, 15-30,15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50, 25-45, 25-40, 25-35,30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,or 50 amino acids in length.

In some embodiments, at least two, three, four, five, six, or morearginine residues present in the synthetic peptide are citrullinated. Inother embodiments, all of the arginine residues present in the syntheticpeptide are citrullinated. In certain instances, at least one, two,three, four, five, six, or more of the cysteine residues present in thesynthetic peptide are substituted with a serine residue, e.g., toprevent disulfide bond formation. In certain other instances, all of thecysteine residues present in the synthetic peptide are substituted witha serine residue.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In a related aspect, the present invention provides a synthetic peptidecomprising an amino acid sequence selected from the group consisting ofSEQ ID NOS:40-355. In one embodiment, the present invention provides asynthetic peptide comprising an amino acid sequence that is at leastabout 80% identical to a peptide selected from the group consisting ofSEQ ID NOS:40-355. In other embodiments, the synthetic peptide may be atleast about 85% identical, or at least about 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to apeptide selected from SEQ ID NOS:40-355.

In certain instances, the synthetic peptide is about 5-50, 8-50, 8-25,8-15, 10-50, 10-45, 10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45,15-40, 15-35, 15-30, 15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50,25-45, 25-40, 25-35, 30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, or 50 amino acids in length.

In certain embodiments, the synthetic peptide is immunologicallyreactive with an autoantibody associated with rheumatoid arthritis.Preferably, the autoantibody associated with rheumatoid arthritis is ananti-citrullinated protein antibody. In certain instances, the syntheticpeptide may further comprise a tag or capture moiety (e.g., biotin), aspacer or linker (e.g., glycine spacer), be labeled (e.g., fluorescentlabel), be amidated (e.g., at the C-terminus), or be otherwisechemically modified.

In another aspect, the present invention provides a method for detectingan anti-citrullinated protein antibody in a biological sample, themethod comprising the steps of:

-   -   (a) contacting the biological sample with a synthetic peptide        described herein under conditions suitable to transform the        synthetic peptide into a complex comprising the synthetic        peptide and the anti-citrullinated protein antibody; and    -   (b) detecting the presence (or absence) or level of said        complex.

Methods of detecting the presence or level of the complex are known inthe art, and include, without limitation, ELISA, mass spectrometry,immunoassays, fluorescence polarization, fluorescence anisotropy,western blotting, size exclusion chromatography, dynamic or static lightscattering, analytical ultracentrifugation, and the like.

Accordingly, in certain embodiments, a detectable moiety may be used tofacilitate detection of the complex. In certain embodiments, thedetectable moiety may be conjugated to the synthetic peptide. In otherembodiments, the detectable moiety may be conjugated to a detectionreagent that binds to the synthetic protein, the anti-citrullinatedprotein antibody, or the complex thereof. In certain embodiments, thedetectable moiety is selected from the group consisting of radioactivegroups, fluorescent groups, luminescent groups, enzymes, biotin, anddyes.

In a related aspect, the present invention provides a method fordetecting an anti-citrullinated protein antibody in a biological sample,the method comprising the steps of:

-   -   (a) contacting the biological sample with a synthetic peptide        described herein under conditions suitable to transform the        synthetic peptide into a complex comprising the synthetic        peptide and the anti-citrullinated protein antibody;    -   (b) contacting the complex with a detection reagent comprising a        reporter group to transform the complex into a labeled complex;        and    -   (c) detecting the presence (or absence) or level of the labeled        complex.

Any biological sample such as a tissue or bodily fluid sample obtainedfrom an individual is suitable for use in the methods of the presentinvention to aid, assist, facilitate, or improve the detection of ACPAs.Non-limiting examples of tissue samples include buccal cells, a brainsample, a skin sample, or an organ sample (e.g., liver). A bodily fluidsample includes all fluids that are present in the body such as, e.g.,blood, plasma, serum, saliva, synovial fluid, lymph, urine, orcerebrospinal fluid. Preferably, the sample is human serum.

In some embodiments, the detection reagent is selected from the groupconsisting of an anti-IgA antibody, an anti-IgG antibody, an anti-IgMantibody, Protein L, Protein A, Protein G, and mixtures thereof. Inother embodiments, the reporter group is selected from the groupconsisting of radioactive groups, fluorescent groups, luminescentgroups, enzymes, biotin, and dyes.

In certain instances, the step of detecting the presence or level of thelabeled complex comprises detecting the presence or level of a signalgenerated from the reporter group, e.g., using a detection device. As anon-limiting example, the detection device may comprise aspectrophotometer.

The assay method of the present invention is useful for aiding in thedetection of IgA anti-citrullinated protein antibodies, IgGanti-citrullinated protein antibodies, IgM anti-citrullinated proteinantibodies, or mixtures thereof. In preferred embodiments, the assaymethod is an enzyme-linked immunosorbent assay (ELISA) method.

In yet another aspect, the present invention provides a method forperforming an assay to aid in the diagnosis or prognosis of rheumatoidarthritis, the method comprising:

-   -   (a) detecting the presence (or absence) or level of an        anti-citrullinated protein antibody in a biological sample by        contacting the sample with a synthetic peptide described herein;        and    -   (b) reporting the presence (or absence) or level of the        anti-citrullinated protein antibody in the sample to aid in the        diagnosis or prognosis of rheumatoid arthritis.

In a related aspect, the present invention provides a method forimproving the sensitivity of diagnosing or prognosing rheumatoidarthritis, the method comprising:

-   -   (a) detecting the presence (or absence) or level of an        anti-citrullinated protein antibody in a biological sample with        a synthetic peptide described herein; and    -   (b) reporting the presence (or absence) or level of the        anti-citrullinated protein antibody in the sample to improve the        sensitivity of diagnosing or prognosing rheumatoid arthritis.

Any of the biological samples described above are suitable for use inthe assay methods of the present invention to aid, assist, facilitate,or improve the diagnosis or prognosis of RA. In a preferred embodiment,the sample is human serum.

In certain embodiments, the step of detecting the presence or level ofanti-citrullinated protein antibodies in the sample is performed usingan ELISA. In some instances, the ELISA comprises the steps of: (a)contacting the sample with an enzyme-labeled immunoglobulin-bindingprotein; (b) contacting the sample with an enzyme substrate; and (c)analyzing the sample using a detection device. In other embodiments, thestep of detecting the presence or level of anti-citrullinated proteinantibodies in the sample is performed using mass spectrometry,immunoassays, fluorescence polarization, fluorescence anisotropy,western blotting, size exclusion chromatography, dynamic or static lightscattering, analytical ultracentrifugation, and the like.

Examples of immunoglobulin-binding proteins include, but are not limitedto, an anti-IgA antibody, an anti-IgG antibody, an anti-IgM antibody,Protein L, Protein A, Protein G, and mixtures thereof A non-limitingexample of a suitable detection device comprises a spectrophotometer. Insome embodiments, the step of analyzing the sample using a detectiondevice comprises measuring the intensity of color from a product ofenzymatic activity of the enzyme substrate. A non-limiting example of asuitable enzyme substrate is 3,3′,5,5′-tetramethylbenzidine (TMB) or anyother chromogenic reagent known in the art.

In some embodiments, the step of reporting the presence or level ofanti-citrullinated protein antibodies in the sample comprises sending orreporting the results to a clinician, e.g., a rheumatologist or ageneral practitioner. In other embodiments, the step of reporting thepresence or level of anti-citrullinated protein antibodies in the samplecomprises recording or storing the results in a computer database orother suitable machine or device for storing information, e.g., at alaboratory.

In certain instances, the present invention may provide a diagnosis ofRA in the form of a probability that an individual has RA or is at riskof developing RA based on the presence or absence of ACPAs in thesample. For example, an individual can have about a 0%, 5%, 10%, 15%,20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%,90%, 95%, or greater probability of having RA or being at risk ofdeveloping RA. In other instances, the present invention may provide aprognosis of RA in an individual based on the presence or level of ACPAsin the sample. As non-limiting examples, the prognosis can be surgery,development of a more severe form of RA, development of a more advancedstage of RA, development of one or more symptoms associated with RA,and/or recovery from the disease.

In certain embodiments, the method further comprises:

-   -   (a) contacting the sample with an anti-rheumatoid factor (RF)        antibody (e.g., immunoglobulin G (IgG)), or antigenic fragment        (e.g., Fc fragment) thereof, under conditions suitable to        transform the anti-rheumatoid factor (RF) antibody, or antigenic        fragment thereof, into a complex comprising the anti-rheumatoid        factor (RF) antibody, or antigenic fragment thereof, and        rheumatoid factor (RF);    -   (b) detecting the presence or level of the complex, thereby        determining the presence or level of rheumatoid factor (RF) in        the sample; and    -   (c) reporting the presence or level of rheumatoid factor (RF) in        the sample to further improve the sensitivity of diagnosing or        prognosing rheumatoid arthritis.

In preferred embodiments, the step of detecting the presence or level ofthe complex is performed using an ELISA. In other embodiments, the stepof detecting the presence or level of the complex comprises massspectrometry, immunoassays, fluorescence polarization, fluorescenceanisotropy, western blotting, size exclusion chromatography, dynamic orstatic light scattering, analytical ultracentrifugation, and the like.

In yet another aspect, the present invention provides an assay fordiagnosing or prognosing rheumatoid arthritis, the assay comprising:

-   -   (a) contacting a sample with a synthetic peptide described        herein under conditions suitable to transform the synthetic        peptide into a complex comprising the synthetic peptide and an        anti-citrullinated protein antibody; and    -   (b) detecting the presence or level of the complex.

In certain embodiments, the step of detecting the presence or level ofthe complex comprises ELISA, mass spectrometry, immunoassays,fluorescence polarization, fluorescence anisotropy, western blotting,size exclusion chromatography, dynamic or static light scattering,analytical ultracentrifugation, and the like.

In a certain embodiment, the method comprises the steps of:

-   -   (a) contacting a sample with a synthetic peptide described        herein under conditions suitable to transform the synthetic        peptide into a complex comprising the synthetic peptide and an        anti-citrullinated protein antibody;    -   (b) contacting the complex with a detection reagent comprising a        reporter group to transform the complex into a labeled complex;    -   (c) detecting the presence or level of the labeled complex,        thereby determining the presence or level of the        anti-citrullinated protein antibody; and    -   (d) associating the presence or level of the anti-citrullinated        protein antibody in the sample with rheumatoid arthritis.

In preferred embodiments, the anti-citrullinated protein antibodies aredetected with an ELISA. In other embodiments, the anti-citrullinatedprotein antibodies are detected with mass spectrometry, an immunoassay,fluorescence polarization, fluorescence anisotropy, western blotting,size exclusion chromatography, dynamic or static light scattering,analytical ultracentrifugation, and the like.

In still yet another aspect, the present invention provides a kitcomprising:

-   -   (a) at least one synthetic peptide described herein; and    -   (b) at least one detectable moiety.

In some embodiments, the detectable moiety is linked to the syntheticpeptide. In certain instances, the detectable moiety is selected fromthe group consisting of radioactive groups, fluorescent groups,luminescent groups, enzymes, biotin, and dyes. In certain otherinstances, the detectable moiety comprises a detection reagentcomprising a reporter group.

In other embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120,125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190,195, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320,330, 340, 350, or all of the synthetic peptides present in the kit areimmobilized on a solid support. Non-limiting examples of solid supportsinclude magnetic or chromatographic matrix particles, the surface of anassay plate (e.g., microtiter wells), pieces of a solid substratematerial or membrane (e.g., plastic, nylon, paper), and the like. Otherexamples of solid supports include, but are not limited to, glass (e.g.,a glass slide), chips, pins, filters, beads (e.g., magnetic beads,polystyrene beads, etc.), other membrane material (e.g., nitrocellulose,polyvinylidene fluoride (PVDF), etc.), fiber bundles, or any othersuitable substrate. The peptides are generally immobilized or restrainedon the solid support via covalent or noncovalent interactions (e.g.,ionic bonds, hydrophobic interactions, hydrogen bonds, Van der Waalsforces, dipole-dipole bonds). In certain instances, the peptidescomprise capture tags (e.g., biotin) which interact with capture agents(e.g., avidin) bound to the solid support. In certain other instances,the kits described herein may comprise a plurality of peptides coupledto the surface of a solid support in different known/addressablelocations.

In certain other instances, the kits described herein may comprise aplurality of anti-rheumatoid factor (RF) antibodies (e.g., IgGs), orantigenic fragments (e.g., Fc fragments) thereof, coupled to the surfaceof a solid support in different known/addressable locations.

In other embodiments, the detection reagent may comprise, for example,an anti-IgA antibody, an anti-IgG antibody, an anti-IgM antibody,Protein L, Protein A, Protein G, and mixtures thereof. Examples ofreporter groups include, without limitation, radioactive groups,fluorescent groups, luminescent groups, enzymes, biotin, dyes, andmixtures thereof.

In a further aspect, the present invention provides an assay method toaid in the detection of rheumatoid factor (RF), the assay methodcomprising:

-   -   (a) contacting a biological sample with an anti-rheumatoid        factor (RF) antibody (e.g., immunoglobulin G (IgG)), or        antigenic fragment (e.g., Fc fragment) thereof, under conditions        suitable to transform the anti-rheumatoid factor (RF) antibody,        or antigenic fragment thereof, into a complex comprising the        anti-rheumatoid factor (RF) antibody, or antigenic fragment        thereof, and rheumatoid factor (RF);    -   (b) contacting the complex with a detection reagent comprising a        reporter group to transform the complex into a labeled complex,        wherein the detection reagent is Protein L; and    -   (c) detecting the presence (or absence) or level of the labeled        complex.

In another aspect, the present invention provides a method for improvingthe sensitivity of diagnosing or prognosing rheumatoid arthritis, themethod comprising:

-   -   (a) contacting a biological sample with an anti-rheumatoid        factor (RF) antibody (e.g., immunoglobulin G (IgG)), or        antigenic fragment (e.g., Fc fragment) thereof, under conditions        suitable to transform the anti-rheumatoid factor (RF) antibody,        or antigenic fragment thereof, into a complex comprising the        anti-rheumatoid factor (RF) antibody, or antigenic fragment        thereof, and rheumatoid factor (RF);    -   (b) contacting the complex with a detection reagent comprising a        reporter group to transform the complex into a labeled complex,        wherein the detection reagent is Protein L;    -   (c) detecting the presence (or absence) or level of the labeled        complex, thereby determining the presence (or absence) or level        of rheumatoid factor in the sample; and    -   (d) reporting the presence (or absence) or level of rheumatoid        factor in the sample to improve the sensitivity of diagnosing or        prognosing rheumatoid arthritis.

Any of the biological samples described above is suitable for use in themethods of the present invention to aid, assist, facilitate, or improvethe detection of RF or the diagnosis or prognosis of RA. In a preferredembodiment, the sample is human serum.

Non-limiting examples of reporter groups include radioactive groups,fluorescent groups, luminescent groups, enzymes, biotin, dyes, andmixtures thereof. In some instances, the step of detecting the presenceor level of the labeled complex comprises detecting the presence orlevel of a signal generated from the reporter group, e.g., using adetection device. The detection device may comprise, for example, aspectrophotometer. Preferably, the assay method is an enzyme-linkedimmunosorbent assay (ELISA) method.

In some embodiments, the step of reporting the presence or level of RFin the sample comprises sending or reporting the results to a clinician,e.g., a rheumatologist or a general practitioner. In other embodiments,the step of reporting the presence or level of RF in the samplecomprises recording or storing the results in a computer database orother suitable machine or device for storing information, e.g., at alaboratory.

In certain instances, the present invention may provide a diagnosis ofRA in the form of a probability that an individual has RA or is at riskof developing RA based on the presence or absence of RF in the sample.For example, an individual can have about a 0%, 5%, 10%, 15%, 20%, 25%,30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, orgreater probability of having RA or being at risk of developing RA. Inother instances, the present invention may provide a prognosis of RA inan individual based on the presence or level of RF in the sample. Asnon-limiting examples, the prognosis can be surgery, development of amore severe form of RA, development of a more advanced stage of RA,development of one or more symptoms associated with RA, and/or recoveryfrom the disease.

In yet another aspect, the present invention provides an ELISA assaymethod, the ELISA assay method comprising:

-   -   (a) contacting a biological sample with an anti-rheumatoid        factor (RF) antibody (e.g., immunoglobulin G (IgG)), or        antigenic fragment (e.g., Fc fragment) thereof, under conditions        suitable to transform the anti-rheumatoid factor (RF) antibody,        or antigenic fragment thereof, into a complex comprising the        anti-rheumatoid factor (RF) antibody, or antigenic fragment        thereof, and rheumatoid factor (RF);    -   (b) contacting the complex with a detection reagent comprising        an enzyme label to transform the complex into a labeled complex,        wherein the detection reagent is Protein L;    -   (c) contacting the labeled complex with an enzyme substrate; and    -   (d) detecting the presence (or absence) or level of the labeled        complex with a detection device.

Any of the biological samples described above is suitable for use in theELISA assay methods of the present invention. In a preferred embodiment,the sample is human serum.

In some embodiments, the anti-rheumatoid factor (RF) antibody (e.g.,IgG), or antigenic fragment (e.g., Fc fragment) thereof, is immobilizedon a solid support. Non-limiting examples of suitable solid supports aredescribed above. In certain instances, the enzyme label compriseshorseradish peroxidase (HRP). In certain other instances, the detectiondevice comprises a spectrophotometer.

In other embodiments, the step of detecting the presence or level of thelabeled complex with a detection device comprises measuring theintensity of color from a product of enzymatic activity of the enzymesubstrate. Examples of suitable enzyme substrates include, but are notlimited to, 3,3′,5,5′-tetramethylbenzidine (TMB) or any otherchromogenic reagent known in the art.

In still yet another aspect, the present invention provides an assay fordiagnosing or prognosing rheumatoid arthritis, the assay comprising:

-   -   (a) contacting a biological sample with an anti-rheumatoid        factor (RF) antibody (e.g., immunoglobulin G (IgG)), or        antigenic fragment (e.g., Fc fragment) thereof, under conditions        suitable to transform the anti-rheumatoid factor (RF) antibody,        or antigenic fragment thereof, into a complex comprising the        anti-rheumatoid factor (RF) antibody, or antigenic fragment        thereof, and rheumatoid factor (RF);    -   (b) contacting the complex with a detection reagent comprising        an enzyme label to transform the complex into a labeled complex,        wherein the detection reagent is Protein L;    -   (c) detecting the presence (or absence) or level of the labeled        complex, thereby determining the presence (or absence) or level        of rheumatoid factor; and    -   (d) associating the presence (or absence) or level of rheumatoid        factor in the sample with rheumatoid arthritis.

In preferred embodiments, the presence or level of rheumatoid factor isdetected with an ELISA. In other embodiments, the presence or level ofrheumatoid factor is detected with mass spectrometry, an immunoassay,fluorescence polarization, fluorescence anisotropy, western blotting,size exclusion chromatography, dynamic or static light scattering,analytical ultracentrifugation, and the like.

In an additional aspect, the present invention provides a kitcomprising:

-   -   (a) an anti-rheumatoid factor (RF) antibody (e.g., IgG), or        antigenic fragment (e.g., Fc fragment) thereof; and    -   (b) a detection reagent optionally comprising a reporter group,        wherein the detection reagent is Protein L.

In some embodiments, the anti-rheumatoid factor (RF) antibody (e.g.,IgG), or antigenic fragment (e.g., Fc fragment) thereof, is immobilizedon a solid support. Non-limiting examples of suitable solid supports aredescribed above. The anti-rheumatoid factor (RF) antibody (e.g., IgG),or antigenic fragment (e.g., Fc fragment) thereof, is generallyimmobilized or restrained on the solid support via covalent ornoncovalent interactions (e.g., ionic bonds, hydrophobic interactions,hydrogen bonds, Van der Waals forces, dipole-dipole bonds). In certaininstances, the anti-rheumatoid factor (RF) antibody (e.g., IgG), orantigenic fragment (e.g., Fc fragment) thereof, comprises capture tags(e.g., biotin) which interact with capture agents (e.g., avidin) boundto the solid support.

In other embodiments, the reporter group may comprise, e.g., radioactivegroups, fluorescent groups, luminescent groups, enzymes, biotin, dyes,and mixtures thereof. In certain instances, the reporter group compriseshorseradish peroxidase (HRP).

In a further aspect, the present invention provides a method foridentifying a peptide that is immunologically reactive with ananti-citrullinated protein antibody, the method comprising:

-   -   (a) identifying at least one antigenic peptide epitope in at        least one synovial fluid polypeptide, wherein the antigenic        peptide epitope is predicted to be immunologically reactive with        an anti-citrullinated protein antibody, wherein the antigenic        peptide epitope contains at least one citrullinated arginine        residue;    -   (b) synthesizing a peptide that comprises at least one of the        antigenic peptide epitopes;    -   (c) contacting a sample from a rheumatoid arthritis (RA)        individual with the peptide under conditions suitable to        transform the peptide into a complex comprising the peptide and        anti-citrullinated protein antibody; and    -   (d) identifying the peptide as being immunologically reactive        with the anti-citrullinated protein antibody based on the        presence or level of the complex.

In one embodiment, step (c) of the above-described method furthercomprises:

-   -   contacting the complex with a detection reagent comprising a        reporter group to transform the complex into a labeled complex;        and    -   detecting the presence (or absence) or level of the labeled        complex.

Examples of synovial fluid polypeptides include, but are not limited to,vimentin, fibrinogen alpha-chain, fibrinogen beta-chain, fibrinogengamma-chain, alpha-enolase, β-actin, aggrecan, gelsolin, lumican,fibronectin, tropomyosin, cartilage oligomeric matrix protein,glucose-6-phosphate isomerase, lamin B1, lamin B2, lamin A/C,myeloblastin (proteinase 3), phospholipid (PL) scramblase 1,apolipoprotein (a), BiP (heat shock 70 kDa protein 5), histone H2A,histone H2B, histone H3, histone H4, COL2A1, COL9A1, COL10A1, COL11A1,COL11A2, syndecan 1, syndecan 3, CD44, intercellular adhesion molecule 1(ICAM1), vascular cell adhesion molecule 1 (VCAM1), glypican 1, glypican2, glypican 4, glypican 5, glypican 6, vitronectin, nidogen, andcombinations thereof.

In certain embodiments, the antigenic peptide epitope comprises at least5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35,40, 45, 50, or more contiguous amino acids of a synovial fluidpolypeptide sequence. Preferably, the antigenic peptide epitopecomprises or consists of 9 contiguous amino acids of a synovial fluidpolypeptide sequence.

In certain other embodiments, the antigenic peptide epitope is predictedto be immunologically reactive with an anti-citrullinated proteinantibody when a score calculated for the antigenic peptide epitope isgreater than or equal to a predetermined score. In certain instances,the score for the antigenic peptide epitope is calculated by adding up avalue given to each amino acid in the antigenic peptide epitope based onthe position and side-chain of the amino acid. In one embodiment, thepeptide epitope comprises at least about 5 amino acids, or at leastabout 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more amino acids. In aspecific embodiment, the peptide epitope is 9 amino acids long. As anon-limiting example, the value given to each amino acid in theantigenic peptide epitope may be a value shown in FIG. 10, wherein thevalue given to each amino acid is dependent upon the position of theamino acid in the peptide epitope sequence and the nature of the aminoacid side-chain.

In certain instances, the predetermined score is +2.0. In certain otherinstances, the predetermined score is 0, +0.5, +1.0, +1.5, +2.0, +2.5,+3.0, +3.5, +4.0, +4.5, +5.0, +5.5, +6.0, +6.5, +7.0, +7.5, +8.0, +8.5,+9.0, +9.5, +10.0, or any fraction thereof. One skilled in the art willunderstand that the predetermined score may vary (e.g., be a positive ornegative value) and will depend upon the specific value assigned to eachamino acid at a particular position in the antigenic peptide epitopesequence.

In some embodiments, at least two, three, four, five, six, or more ofthe arginine residues present in the antigenic peptide epitope orepitopes are substituted with a citrulline residue. In otherembodiments, all of the arginine residues present in the antigenicpeptide epitope or epitopes are substituted with a citrulline residue.

Peptides comprising at least one, two, three, four, five, six, or moreof the antigenic peptide epitopes identified in step (a) may besynthesized using any technique known in the art. Non-limiting examplesof suitable peptide synthesis techniques are described below and includeclassical chemical synthesis and synthesis by recombinant means.Peptides may be linear or cyclized. For example, a peptide containingthree of the antigenic peptide epitopes identified in step (a) may belinked by peptide bonds, such that a first peptide epitope is linked toa second peptide epitope by a peptide bond, which is linked to a thirdpeptide epitope by a peptide bond, with the resulting peptide having alinear structure.

In certain embodiments, the detection reagent may comprise, for example,an anti-IgA antibody, an anti-IgG antibody, an anti-IgM antibody,Protein L, Protein A, Protein G, and mixtures thereof. Examples ofreporter groups include, without limitation, radioactive groups,fluorescent groups, luminescent groups, enzymes, biotin, dyes, andmixtures thereof.

In some instances, the step of detecting the presence or level of thelabeled complex comprises detecting the presence or level of a signalgenerated from the reporter group, e.g., using a detection device. Thedetection device may comprise, e.g., a spectrophotometer.

The method described above is particularly useful for identifyingpeptides that are immunologically reactive with IgA anti-citrullinatedprotein antibodies, IgG anti-citrullinated protein antibodies, IgManti-citrullinated protein antibodies, or mixtures thereof.

Example 4 provides an exemplary embodiment of the method described abovefor predicting antigenic peptide epitopes in polypeptides present insynovial fluid and identifying novel citrullinated peptides based uponone or more predicted antigenic peptide epitopes.

In an additional aspect, the present invention provides a syntheticpeptide identified by the method described above. In certainembodiments, the citrullinated peptides identified using theabove-described method are useful for detecting anti-citrullinatedprotein antibodies present in an individual's sample with improvedsensitivity and/or specificity, thereby enabling the early detectionand/or prognosis of RA.

In some embodiments, the synthetic peptide is from 5-50, 8-50, 8-25,8-15, 10-50, 10-45, 10-40, 10-35, 10-30, 10-25, 10-20, 15-50, 15-45,15-40, 15-35, 15-30, 15-25, 20-50, 20-45, 20-40, 20-35, 20-30, 25-50,25-45, 25-40, 25-35, 30-50, 30-45, 30-40, 35-50, 35-45, 40-50, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, or 50 amino acids in length. In otherembodiments, the peptide further comprises a tag (e.g., biotin).

In another aspect, the present invention provides a kit comprising:

-   -   (a) at least one synthetic peptide identified by the method        described above; and    -   (b) a detection reagent comprising a reporter group.

In a related embodiment, the present invention provides a kitcomprising:

-   -   (a) at least one synthetic peptide identified by the method        described above; and    -   (b) a detectable moiety.

In certain embodiments, the detectable moiety may be conjugated to thesynthetic peptide. In other embodiments, the detectable moiety may beconjugated to a detection reagent that binds to the synthetic protein,the anti-citrullinated protein, or the complex thereof. In certainembodiments, the detectable moiety is selected from the group consistingof radioactive groups, fluorescent groups, luminescent groups, enzymes,biotin, dyes, or a combination thereof.

In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125,130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195,200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330,340, 350, or all of the synthetic peptides present in the kit areimmobilized on a solid support. Non-limiting examples of suitable solidsupports are described above. The peptides are generally immobilized orrestrained on the solid support via covalent or noncovalent interactions(e.g., ionic bonds, hydrophobic interactions, hydrogen bonds, Van derWaals forces, dipole-dipole bonds). In certain instances, the peptidescomprise capture tags (e.g., biotin) which interact with capture agents(e.g., avidin) bound to the solid support. In certain other instances,the kits described herein may comprise a plurality of peptides coupledto the surface of a solid support in different known/addressablelocations.

In other embodiments, the detection reagent may comprise, for example,an anti-IgA antibody, an anti-IgG antibody, an anti-IgM antibody,Protein L, Protein A, Protein G, and mixtures thereof. Examples ofreporter groups include, without limitation, radioactive groups,fluorescent groups, luminescent groups, enzymes, biotin, dyes, andmixtures thereof.

IV. Methods of Peptide Synthesis

In some embodiments, the present invention provides a method forproducing a peptide described herein by classical chemical synthesis,wherein citrulline residues are substituted for arginine residues atcertain steps during the chemical synthesis. In other embodiments, thepresent invention provides a method for producing a peptide describedherein, wherein the primary amino acid sequence is produced by classicalchemical synthesis, and wherein at least one arginine residue issubsequently transformed to a citrulline residue by contacting thepeptide with a peptidylarginine deiminase (PAD).

The peptides of the present invention may be prepared using methodsknown in the art. For example, peptides may be produced by chemicalsynthesis, e.g., using solid phase techniques and/or automated peptidesynthesizers. In certain instances, peptides may be synthesized usingsolid phase strategies on an automated multiple peptide synthesizer(Abimed AMS 422) using 9-fluorenylmethyloxycarbonyl (Fmoc) chemistry.The synthesized peptides can then be isolated and/or purified byreversed phase-HPLC and lyophilized. Peptides may also be preparedaccording to the solid phase methods described by Atherton and Shepard,in “Solid phase peptide synthesis,” IRL Press, Oxford, UK (1989).Peptide synthesis may alternatively be carried out in homogeneoussolution. For example, the synthesis technique in homogeneous solutiondescribed by Houbenweyl, in “Methode der Organischen Chemie,” edited byE. Wunsch, vol. 15-1 et 11, Thieme, Stuttgart, Germany (1974), can beused. The claimed peptides may be obtained by substituting the originalarginine residues with citrulline residues during chemical synthesis, orby contacting the peptides after synthesis with a peptidylargininedeiminase of any eukaryotic origin.

In certain embodiments, peptides may be produced by recombinant means,e.g., using recombinant DNA techniques described by Sambrook et al., in“Molecular Cloning, A Laboratory Manual,” 2nd edition, Cold SpringHarbor University Press, Cold Spring Harbor, N.Y. USA (1989) or Stemmeret al., Gene, 164:49-53 (1995), in prokaryotes or lower or highereukaryotes. The term “lower eukaryote” includes host cells such asyeast, fungi, and the like. Lower eukaryotes are generally (but notnecessarily) unicellular. Examples of lower eukaryotic host cellsinclude, but are not limited to, yeast, particularly species withinSchizosaccharomyces, Saccharomyces, Kluiveromvces, Pichia (e.g., Pichiapastoris), Hansenula (e.g., Hansenula polymorpha), Schwaniomyces,Schizosaccharomyces, Yarowia, Zygosaccharomyces, and the like. The term“higher eukaryote” includes host cells derived from higher animals, suchas mammals, reptiles, insects, and the like. Examples of highereukaryotic host cells include Chinese hamster cell lines (e.g., CHOcells), monkey cell lines (e.g., COS and Vero cells), baby hamsterkidney cell lines (BHK cells), pig kidney cell lines (PK15 cells),rabbit kidney cell lines (RK13 cells), the human osteosarcoma cell line143 B, the human cell line HeLa, human hepatoma cell lines like Hep G2,and insect cell lines (e.g., Spodoptera frugiperda). The term“prokaryote” includes hosts such as E. coli, Lactobacillus, Lactococcus,Salmonella, Streptococcus, Bacillus subtilis, or Streptomyces. Incertain instances, the present invention provides host cells comprisingan expression vector for one or more the peptides described herein. Thehost cells may be provided in suspension or flask cultures, tissuecultures, organ cultures, and the like. Alternatively, the host cellsmay be derived from transgenic animals. In some embodiments, the claimedpeptides are obtained by contacting the recombinant peptides afterisolation and/or purification from host cells with a peptidylargininedeiminase of any eukaryotic origin.

Peptides may alternatively be prepared by cleavage of a longerpolypeptide or full-length protein sequence. The peptides describedherein may then be obtained by contacting the peptide fragment aftercleavage with a peptidylarginine deiminase of any eukaryotic origin. Forexample, a peptide fragment of the present invention that isimmunologically reactive with an RA-associated autoantibody may beobtained by first cleaving any one of the proteins set forth in SEQ IDNOS:1-39 by contacting the protein with an endopeptidase under suitableconditions and then contacting the resulting peptide fragment ofinterest with a peptidylarginine deiminase under suitable conditions totransform at least one of the arginine residues present in the peptidesequence to a citrulline residue.

In other embodiments, the peptides of the present invention may becyclized. Methods are well known in the art for introducing cyclicstructures into peptides to select and provide conformationalconstraints to the structure that result in enhanced stability. Forexample, a C- or N-terminal cysteine can be added to the peptide, sothat when oxidized the peptide will contain a disulfide bond, generatinga cyclic peptide. Other peptide cyclization methods include theformation of thioethers and carboxyl- and amino-terminal amides andesters. A number of synthetic techniques have been developed to generatesynthetic circular peptides (see, e.g., Tarn et al., Protein Sci.,7:1583-1592 (1998); Romanovskis et al., J. Pept. Res., 52: 356-374(1998); Camarero et al., J. Amer. Chem. Soc., 121: 5597-5598 (1999);Valero et al., J. Pept. Res., 53(1): 56-67 (1999)). Generally, the roleof cyclizing peptides is two fold: (1) to reduce hydrolysis in vivo; and(2) to thermodynamically destabilize the unfolded state and promotesecondary structure formation.

V. Antibodies

In some embodiments, the present invention provides an antibody raisedupon immunization with any of the citrullinated peptides describedherein, wherein the antibody is specifically immunoreactive with thecitrullinated peptide. In other embodiments, the present inventionprovides an anti-idiotype antibody raised upon immunization with anRA-associated antibody, wherein the anti-idiotype antibody isspecifically immunoreactive with the RA-associated antibody, therebymimicking any of the citrullinated peptides described herein. Theseantibodies may be polyclonal or monoclonal.

To prepare the antibodies of the present invention, a host animal may beimmunized with any of the citrullinated peptides or RA-associatedantibodies described herein in a pharmaceutically acceptable carrier.Examples of pharmaceutically acceptable carriers include, but are notlimited to, any carrier that does not itself induce the production ofantibodies harmful to the individual receiving the composition. Suitablecarriers are typically large, slowly metabolized macromolecules such asproteins, polysaccharides, polylactic acids, polyglycolic acids,polymeric amino acids, and amino acid copolymers as well as inactivevirus particles. Such carriers are well known to those of ordinary skillin the art.

Preferred adjuvants to enhance effectiveness of the composition include,but are not limited to, aluminum hydroxide (alum),N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP) as described inU.S. Pat. No. 4,606,918, N-acetyl-normuramyl-L-alanyl-D-isoglutamine(nor-MDP),N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine(MTP-PE), and RIBI (which contains three components extracted frombacteria—monophosphoryl lipid A, trehalose dimycolate, and cell wallskeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion). Any of the 3components MPL, TDM or CWS may also be used alone or combined 2 by 2.Additionally, adjuvants such as Stimulon (Cambridge Bioscience;Worcester, Mass.) or SAF-1 (Syntex) may be used. Further, CompleteFreund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA) may beused for non-human applications and research purposes.

The immunogenic compositions typically containpharmaceutically-acceptable vehicles, such as water, saline, glycerol,ethanol, etc. Additionally, auxiliary substances, such as wetting oremulsifying agents, pH buffering substances, preservatives, and thelike, may be included in such vehicles. The term “immunogenic” includesthe ability of a substance to cause a humoral and/or cellular response,whether alone or when linked to a carrier, in the presence or absence ofan adjuvant.

In some embodiments, the immunogenic compositions are prepared asinjectables, either as liquid solutions or suspensions. Solid formssuitable for solution in, or suspension in, liquid vehicles prior toinjection may also be prepared. The preparation also may be emulsifiedor encapsulated in liposomes for enhanced adjuvant effect. The antigenmay also be incorporated into immune-stimulating complexes together withsaponins, for example, Quil A (ISCOMS).

Immunogenic compositions used to raise antibodies comprise a “sufficientamount” or an “immunologically effective amount” of the antigen, as wellas any other of the above-mentioned components, as needed. Animmunologically effective amount includes situations where theadministration of that amount to a host animal, either in a single doseor as part of a series of doses, is effective to provoke an immuneresponse and to raise antibodies against the antigen (e.g.,citrullinated peptide or RA-associated antibody). This amount variesdepending upon the health and physical condition of the host animal, thetaxonomic group of the host animal (e.g., nonhuman primate, primate,rabbit, rat, mouse, etc.), the capacity of the host animal's immunesystem to synthesize antibodies, the immunogenicity of the antigen, itsmode of administration, and other relevant factors. It is expected thatthe amount will fall into a relatively broad range that can bedetermined through routine trials. Usually, the amount will vary fromabout 0.01 to about 1000 mg/dose, more particularly from about 0.1 toabout 100 mg/dose.

In certain embodiments, the immunogenic compositions may beconventionally administered parenterally, typically by injection, forexample, subcutaneously, intravenously, or intramuscularly. Additionalformulations suitable for other methods of administration include oralformulations and suppositories. Dosages may be administered as a singledose schedule or following a multiple dose schedule. The immunogeniccompositions may be administered in conjunction with otherimmunoregulatory agents.

The host serum or plasma is collected following an appropriate timeinterval to provide a composition comprising antibodies reactive withthe peptides or RA-associated antibodies of the present invention. Thegamma globulin fraction or the IgG antibodies can be obtained, forexample, by use of saturated ammonium sulfate or DEAE Sephadex, or othertechniques known to those skilled in the art.

Monoclonal antibodies may be produced by any hybridoma formed accordingto classical methods from the spleen cells of an animal, particularlyfrom a mouse or rat, that is immunized against an antigen, and of cellsof a myeloma cell line, wherein the hybridoma is selected by its abilityto produce monoclonal antibodies recognizing the antigen initially usedfor immunization of the animal.

In certain instances, monoclonal antibodies may be humanized versions ofmouse monoclonal antibodies made by means of recombinant DNA technology,departing from parts of mouse and/or human genomic DNA sequences codingfor H and L chains or from cDNA clones coding for H and L chains.Alternatively, monoclonal antibodies may be human monoclonal antibodies.Such antibodies can also be derived from human peripheral bloodlymphocytes of patients with RA. As a non-limiting example, humanmonoclonal antibodies may be prepared by means of human peripheral bloodlymphocyte repopulation of severe combined immune deficiency (SCID) mice(Duchosal et al., Nature, 355:258 (1992)) or by screening vaccinatedhost animals for the presence of reactive B-cells using the antigen.

The present invention also provides truncated versions or single-chainversions of the antibodies and anti-idiotype antibodies described abovethat have retained their original specificity for reacting with theantigen initially used for immunization.

The present invention also provides a method for detecting RA-associatedantibodies from an individual's sample that specifically bind to thepeptides or anti-idiotype antibodies described herein, the methodcomprising: (i) contacting the sample to be analyzed for the presence(or absence) or level of the RA-associated antibodies with a peptide oranti-idiotype antibody as defined above (e.g., under conditions suitableto transform the peptide or anti-idiotype antibody into a complexbetween the peptide or anti-idiotype antibody and the RA-associatedantibody); and (ii) detecting the presence (or absence) or level of thecomplex formed between the peptide or anti-idiotype antibody and theRA-associated antibody. These methods are particularly useful for aidingin, assisting in, or improving the sensitivity of a diagnosis orprognosis of rheumatoid arthritis.

In further embodiments, the present invention provides a reverse methodfor detecting the peptides and/or anti-idiotype antibodies of thepresent invention with RA-associated antibodies from an individual'ssample that specifically bind to the peptides and/or anti-idiotypeantibodies that mimic such peptides, the method comprising: (i)contacting the sample to be analyzed for the presence (or absence) orlevel of a peptide or anti-idiotype antibody described herein with anRA-associated antibody (e.g., under conditions suitable to transform theRA-associated antibody into a complex between the RA-associated antibodyand the peptide or anti-idiotype antibody); and (ii) detecting thepresence (or absence) or level of the complex formed between theRA-associated antibody and the peptide or anti-idiotype antibody. Thesemethods are also useful for aiding in, assisting in, or improving thesensitivity of a diagnosis or prognosis of rheumatoid arthritis.

VI. Assays

Any of a variety of assays, techniques, and kits known in the art can beused to detect the presence (or absence) or level of RA-associatedautoantibodies such as anti-citrullinated protein antibodies (ACPAs) orrheumatoid factor (RF) in a sample from an individual, e.g., to providea clinician with guidance when making a diagnosis or prognosis of RA.

The present invention relies, in part, on detecting the presence (orabsence) or level of at least one antibody or antibody complex in asample obtained from an individual. In preferred embodiments, thepresence (or absence) or level of at least one autoantibody associatedwith RA is detected in an individual's sample. In certain embodiments,RA-associated autoantibodies may be detected in an individual's sampleby detecting the presence (or absence) or level of complexes formedbetween the autoantibody, an antigen specific for the autoantibody, anda suitable detection reagent (e.g., an antibody or protein specific forthe autoantibody that comprises a reporter group).

As used herein, the term “detecting the presence or absence” includesdetecting, measuring, or determining the presence or absence of eachantibody or antibody complex of interest by using any quantitative orqualitative assay known to one of skill in the art. As used herein, theterm “detecting the level” includes detecting, measuring, or determiningthe level of each antibody or antibody complex of interest by using anydirect or indirect quantitative assay known to one of skill in the art.In certain instances, quantitative assays that determine, for example,the relative or absolute amount of an antibody of interest are suitablefor use in the present invention. One skilled in the art will appreciatethat any assay useful for detecting the level of an antibody or antibodycomplex is also useful for detecting its presence or absence.

Flow cytometry can be used to determine the presence or level ofRA-associated autoantibodies in a sample from an individual. Such flowcytometric assays, including bead based immunoassays, can be used todetermine, e.g., ACPA or RF levels in the same manner as described fordetecting serum antibodies to Candida albicans and HIV proteins (see,e.g., Bishop and Davis, J. Immunol. Methods, 210:79-87 (1997); McHugh etal., J. Immunol. Methods, 116:213 (1989); Scillian et al., Blood,73:2041 (1989)).

Phage display technology for expressing a recombinant antigen specificfor RA-associated autoantibodies can also be used to determine thepresence or level of ACPAs or RF in a sample. As a non-limiting example,phage particles expressing an antigen specific for, e.g., one or moreACPAs can be anchored, if desired, to a multi-well plate using anantibody such as an anti-phage monoclonal antibody (Felici et al.,“Phage-Displayed Peptides as Tools for Characterization of Human Sera”in Abelson (Ed.), Methods in Enzymol., 267, San Diego Academic Press,Inc. (1996)).

According to a specific embodiment, the methods of the present inventioncomprise the detection of the presence or level of RA-associatedautoantibodies such as ACPAs or RF in a sample by immunoassayImmunoassays can be based on detecting the binding with an antigen orpool of antigens known to be recognized by these antibodies, e.g., anatural or synthetic citrullinated peptide or an anti-idiotype antibodyfor detecting ACPAs or an immunoglobulin G (IgG) or Fc fragment thereoffor detecting RF. Binding to the antigen can be detected, e.g., by alabeled secondary antibody, e.g., a fluorescently labeled secondaryantibody. Immunoassays may be either competitive or noncompetitive.Non-competitive immunoassays are assays in which the amount of capturedanalyte is directly measured. In competitive assays, the amount ofanalyte present in the sample is measured indirectly by measuring theamount of an added (exogenous) analyte displaced (or competed away) froma capture agent by the analyte present in the sample. Suitableimmunological methods include, but are not limited to, enzyme-linkedimmunosorbent assays (ELISA), immunoblotting, immunospotting (such asline immunoassays or LIA), radioimmunoassays (RIA), fluid or gelprecipitation reactions, immunodiffusion (single or double),agglutination assays, immunoelectrophoresis, time-resolvedimmunofluorometric assays (TRIFMA), Western blots, complement-fixationassays, immunoradiometric assays, fluorescent immunoassays, protein Aimmunoassays, and immunoPCR. An overview of different immunoassays isprovided in, e.g., Self and Cook (Curr. Opin. Biotechnol., 7:60-65(1996)), Wild (Nature Press, London, UK (2001)), Ghindilis et al.(Humana Press, Totowa, N.J., US (2002)), and Kilpatrick (TransfusionMedicine, 12:335-351 (2002)).

Additional immunoassays suitable for use in the present inventioninclude, without limitation, enzyme immunoassays (EIA) such as enzymemultiplied immunoassay technique (EMIT), antigen capture ELISA, sandwichELISA, IgM antibody capture ELISA (MAC ELISA), and microparticle enzymeimmunoassay (MEIA); capillary electrophoresis immunoassays (CEIA);immunoradiometric assays (IRMA); fluorescence polarization immunoassays(FPIA); and chemiluminescence assays (CL). If desired, such immunoassayscan be automated Immunoassays can also be used in conjunction with laserinduced fluorescence (see, e.g., Schmalzing and Nashabeh,Electrophoresis, 18:2184-2193 (1997); Bao, J. Chromatogr. B. Biomed.Sci., 699:463-480 (1997)). Liposome immunoassays, such as flow-injectionliposome immunoassays and liposome immunosensors, are also suitable foruse in the present invention (see, e.g., Rongen et al., J. Immunol.Methods, 204:105-133 (1997)). In addition, nephelometry assays, in whichthe formation of protein/antibody complexes results in increased lightscatter that is converted to a peak rate signal as a function of themarker concentration, are suitable for use in the present invention.Nephelometry assays are commercially available from Beckman Coulter(Brea, Calif.; Kit #449430) and can be performed using a BehringNephelometer Analyzer (Fink et al., J. Clin. Chem. Clin. Biol. Chem.,27:261-276 (1989)).

Antigen capture ELISA can be useful for determining the presence orlevel of one or more RA-associated autoantibodies in a sample. Forexample, in an antigen capture ELISA, an anti-idiotype antibody directedto an ACPA of interest is bound to a solid phase and sample is addedsuch that the ACPA is bound by the anti-idiotype antibody. After unboundproteins are removed by washing, the amount of bound ACPA can bequantitated using, e.g., a radioimmunoassay (see, e.g., Harlow and Lane,Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, NewYork, 1988)). Sandwich ELISA can also be suitable for use in the presentinvention. For example, in a two-antibody sandwich assay, a firstanti-idiotype antibody is bound to a solid support, and the ACPA ofinterest is allowed to bind to the first antibody. The amount of theACPA is quantitated by measuring the amount of a second anti-idiotypeantibody that binds the ACPA. The antibodies can be immobilized onto avariety of solid supports, such as magnetic or chromatographic matrixparticles, the surface of an assay plate (e.g., microtiter wells),pieces of a solid substrate material or membrane (e.g., plastic, nylon,paper), and the like. An assay strip can be prepared by coating theantibody or a plurality of antibodies in an array on a solid support.This strip can then be dipped into the test sample and processed quicklythrough washes and detection steps to generate a measurable signal, suchas a colored spot.

A radioimmunoassay using, for example, an iodine-125 (¹²⁵I) orchemiluminescent labeled secondary antibody (Harlow and Lane, supra) isalso suitable for determining the presence or level of one or moreRA-associated autoantibodies in a sample. In certain instances, achemiluminescence assay using a chemiluminescent secondary antibody issuitable for sensitive, non-radioactive detection of ACPA or RF levels.Such secondary antibodies can be obtained commercially from varioussources, e.g., Amersham Lifesciences, Inc. (Arlington Heights, Ill.).

Specific immunological binding of the antigen or pool of antigens to theRA-associated autoantibody of interest can be detected directly orindirectly. Direct labels include fluorescent or luminescent tags,metals, dyes, radionuclides, and the like, attached to the antibody. Anantigen or pool of antigens labeled with iodine-125 (¹²⁵I) can be usedfor determining the level of ACPAs or RF in a sample. Achemiluminescence assay using a chemiluminescent antigen is suitable forsensitive, non-radioactive detection of ACPAs or RF levels. An antigenlabeled with a fluorochrome is also suitable for determining the levelsof ACPAs or RF in a sample. Examples of fluorochromes include, withoutlimitation, DAPI, fluorescein, Hoechst 33258, R-phycocyanin,B-phycoerythrin, R-phycoerythrin, rhodamine, Texas red, and lissamine.Secondary antibodies linked to fluorochromes can be obtainedcommercially, e.g., goat F(ab′)₂ anti-human IgG-FITC is available fromTago Immunologicals (Burlingame, Calif.).

Indirect labels include various enzymes well-known in the art, such ashorseradish peroxidase (HRP), alkaline phosphatase (AP),β-galactosidase, urease, and the like. A horseradish-peroxidasedetection system can be used, for example, with the chromogenicsubstrate tetramethylbenzidine (TMB), which yields a soluble product inthe presence of hydrogen peroxide that is detectable at 450 nm. Analkaline phosphatase detection system can be used with the chromogenicsubstrate p-nitrophenyl phosphate, for example, which yields a solubleproduct readily detectable at 405 nm. Similarly, a β-galactosidasedetection system can be used with the chromogenic substrateo-nitrophenyl-β-D-galactopyranoside (ONPG), which yields a solubleproduct detectable at 410 nm. An urease detection system can be usedwith a substrate such as urea-bromocresol purple (Sigma Immunochemicals;St. Louis, Mo.). A useful secondary antibody linked to an enzyme can beobtained from a number of commercial sources, e.g., goat F(ab′)₂anti-human IgG-alkaline phosphatase can be purchased from JacksonImmunoResearch (West Grove, Pa.).

A signal from the direct or indirect label can be analyzed, for example,using a spectrophotometer to detect color from a chromogenic substrate;a radiation counter to detect radiation such as a gamma counter fordetection of ¹²⁵I; or a fluorometer to detect fluorescence in thepresence of light of a certain wavelength. For detection ofenzyme-linked antibodies, a quantitative analysis of the amount of ACPAor RF levels can be made using a spectrophotometer such as an EMAXMicroplate Reader (Molecular Devices; Menlo Park, Calif.) in accordancewith the manufacturer's instructions. If desired, the assays of thepresent invention can be automated or performed robotically, and thesignal from multiple samples can be detected simultaneously.

Quantitative western blotting can also be used to detect or determinethe presence or level of one or more RA-associated autoantibodies in asample. Western blots can be quantitated by well-known methods such asscanning densitometry or phosphorimaging. As a non-limiting example,protein samples are electrophoresed on 10% SDS-PAGE Laemmli gels.Primary murine monoclonal antibodies are reacted with the blot, andantibody binding can be confirmed to be linear using a preliminary slotblot experiment. Goat anti-mouse horseradish peroxidase-coupledantibodies (BioRad) are used as the secondary antibody, and signaldetection performed using chemiluminescence, for example, with theRenaissance chemiluminescence kit (New England Nuclear; Boston, Mass.)according to the manufacturer's instructions. Autoradiographs of theblots are analyzed using a scanning densitometer (Molecular Dynamics;Sunnyvale, Calif.) and normalized to a positive control. Values arereported, for example, as a ratio between the actual value to thepositive control (densitometric index). Such methods are well known inthe art as described, for example, in Parra et al., J. Vasc. Surg.,28:669-675 (1998).

Alternatively, a variety of immunohistochemical assay techniques can beused to determine the presence or level of one or more RA-associatedautoantibodies in a sample. As used herein, the term immunohistochemicalassay encompasses techniques that utilize the visual detection offluorescent dyes or enzymes coupled (i.e., conjugated) to antibodiesthat react with the RA-associated autoantibody of interest (e.g., ACPAor RF) using fluorescent microscopy or light microscopy and includes,without limitation, direct fluorescent antibody assay, indirectfluorescent antibody (IFA) assay, anticomplement immunofluorescence,avidin-biotin immunofluorescence, and immunoperoxidase assays. Theconcentration of an ACPA or RF in a sample can be quantitated, e.g.,through endpoint titration or through measuring the visual intensity offluorescence compared to a known reference standard.

Alternatively, the presence or level of an RA-associated autoantibody(e.g., ACPA or RF) can be determined by detecting or quantifying theamount of the purified autoantibody. Purification of the autoantibodycan be achieved, for example, by high pressure liquid chromatography(HPLC), alone or in combination with mass spectrometry (e.g., MALDI/MS,MALDI-TOF/MS, SELDI-TOF/MS, tandem MS, etc.). Qualitative orquantitative detection of an autoantibody of interest can also bedetermined by well-known methods including, without limitation, Bradfordassays, Coomassie blue staining, silver staining, assays forradiolabeled protein, and mass spectrometry.

The analysis of a plurality of RA-associated autoantibody markers may becarried out separately or simultaneously with one test sample. Forseparate or sequential assay of RA-associated autoantibodies, suitableapparatuses include clinical laboratory analyzers such as the ElecSys(Roche), the AxSym (Abbott), the Access (Beckman), the ADVIA®, theCENTAUR® (Bayer), and the NICHOLS ADVANTAGE® (Nichols Institute)immunoassay systems. Preferred apparatuses or protein chips performsimultaneous assays of a plurality of autoantibody markers on a singlesurface. Particularly useful physical formats comprise surfaces having aplurality of discrete, addressable locations for the detection of aplurality of different autoantibody markers. Such formats includeprotein microarrays, or “protein chips” (see, e.g., Ng et al., J. CellMol. Med., 6:329-340 (2002)) and certain capillary devices (see, e.g.,U.S. Pat. No. 6,019,944). In these embodiments, each discrete surfacelocation may comprise an antigen or a plurality of antigens toimmobilize ACPAs or RF for detection at each location. Surfaces mayalternatively comprise one or more discrete particles (e.g.,microparticles or nanoparticles) immobilized at discrete locations of asurface, where the microparticles comprise an antigen or a plurality ofantigens to immobilize ACPAs or RF for detection.

Several RA-associated autoantibody markers of interest may be combinedinto one test for efficient processing of a multiple of samples. Inaddition, one skilled in the art would recognize the value of testingmultiple samples (e.g., at successive time points, etc.) from the samesubject. Such testing of serial samples can allow the identification ofchanges in ACPA or RF levels over time. Increases or decreases in ACPAor RF levels, as well as the absence of change in ACPA or RF levels, canprovide useful information to guide treatment decisions during thecourse of therapy.

A panel for measuring one or more of RA-associated autoantibodies may beconstructed to provide relevant information related to the approach ofthe present invention for diagnosing or prognosing RA. Such a diagnosticor prognostic panel may be constructed to determine the presence orlevel of RF and/or the presence or level of 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55,60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170,180, 190, 200, or more individual ACPAs that are present in anindividual's sample. The analysis of a single marker or subsets ofmarkers can also be carried out by one skilled in the art in variousclinical settings. These include, but are not limited to, ambulatory,urgent care, critical care, intensive care, monitoring unit, inpatient,outpatient, physician office, medical clinic, and health screeningsettings.

The analysis of RA-associated autoantibody markers may be carried out ina variety of physical formats as well. For example, the use ofmicrotiter plates or automation could be used to facilitate theprocessing of large numbers of test samples. Alternatively, singlesample formats could be developed to facilitate treatment, diagnosis,and prognosis in a timely fashion.

VII. Kits

The present invention also provides kits to facilitate and/orstandardize the use of the compositions provided herein, as well as tofacilitate the methods or assays described herein. Materials andreagents to carry out these various methods or assays can be provided inkits to facilitate their execution. As used herein, the term “kit”includes a combination of articles that facilitates a method, process,assay, analysis, or manipulation. In particular, kits comprising thepeptides of the present invention find utility in a wide range ofapplications including, but not limited to, detecting the presence (orabsence) or level of one or more RA-associated antibodies such asanti-citrullinated protein antibodies (ACPAs) and/or rheumatoid factor(RF) to provide a sensitive and specific diagnosis, classification,and/or prognosis of rheumatic diseases such as rheumatoid arthritis.

Kits can contain chemical reagents (e.g., citrullinated peptides,labeled antibodies, etc.) as well as other components. In addition, thekits of the present invention can include, without limitation,instructions to the kit user (e.g., directions for use of the peptidesdescribed herein for performing diagnostic or prognostic assays, etc.),apparatus and reagents for sample collection and/or purification,apparatus and reagents for product collection and/or purification,reagents for bacterial cell transformation, reagents for eukaryotic celltransfection, previously transformed or transfected host cells, sampletubes, holders, trays, racks, dishes, plates, solutions, buffers orother chemical reagents, suitable samples to be used forstandardization, normalization, and/or control samples. Kits of thepresent invention can also be packaged for convenient storage and safeshipping, for example, in a box having a lid.

In some embodiments, the present invention provides a diagnostic orprognostic kit for use in detecting autoimmune diseases such as RA,wherein said kit comprises at least one of the above-mentioned peptidesor antibodies. In certain instances, the peptide or antibody is bound toa solid support. In other embodiments, the kit comprises a plurality ofthe peptides and/or antibodies described herein, optionally incombination with other epitopes useful in characterizing ordifferentiating autoimmune diseases, wherein the peptides, antibodiesand/or other epitopes are attached to specific locations on a solidsubstrate. In certain instances, the solid support is a membrane stripand the peptides, antibodies and/or other epitopes are coupled to themembrane in the form of parallel lines. In other instances, certainpeptides, antibodies and/or other epitopes as defined above are notattached to a solid support but are instead provided in the bindingsolution to be used as competitors and/or to block other antibodies thatare present in the sera of patients with autoimmune diseases other thanrheumatoid arthritis, thereby decreasing or eliminating possiblecross-reaction and/or non-specific binding.

In certain instances, the present invention provides a diagnostic orprognostic kit that allows differentiation between those autoimmunediseases in which the characteristic antibodies often cross-react withthe same antigen, thus resulting in difficult and/or slow diagnosis orprognostication. Such kits may be prepared by the simultaneous use ofseveral peptides and/or anti-idiotype antibodies of the presentinvention.

In certain other instances, the present invention provides a diagnosticor prognostic kit for use in detecting the presence or absence ofRA-associated antibodies (e.g., anti-citrullinated protein antibodiesand/or rheumatoid factor). Preferably, the kit comprises at least onepeptide or anti-idiotype antibody described herein, optionally bound toa solid support.

In yet other instances, the present invention provides a diagnostic orprognostic kit for use in determining the type of autoimmune disease.The kit may comprise at least one peptide or anti-idiotype antibodydescribed herein, optionally bound to a solid support.

In further instances, the present invention provides a diagnostic orprognostic kit comprising a plurality of the peptides and/oranti-idiotype antibodies described herein, which are attached tospecific locations on a solid support.

VIII. Therapy and Therapeutic Monitoring

Once a diagnosis or prognosis of RA is made based on the presence orlevel of anti-citrullinated protein antibodies (ACPAs) and/or rheumatoidfactor (RF) in an individual's sample as described herein, the methodsof the present invention may further comprise administering to theindividual a therapeutically effective amount of a drug useful fortreating one or more symptoms associated with RA (i.e., an RA drug). Fortherapeutic applications, the RA drug can be administered alone orco-administered in combination with one or more additional RA drugsand/or one or more drugs that reduce the side-effects associated withthe RA drug. The present invention advantageously enables a clinician topractice “personalized medicine” by guiding treatment decisions andinforming therapy selection for RA such that the right drug is given tothe right patient at the right time.

RA drugs can be administered with a suitable pharmaceutical excipient asnecessary and can be carried out via any of the accepted modes ofadministration. Thus, administration can be, for example, intravenous,topical, subcutaneous, transcutaneous, transdermal, intramuscular, oral,buccal, sublingual, gingival, palatal, intra joint, parenteral,intra-arteriole, intradermal, intraventricular, intracranial,intraperitoneal, intralesional, intranasal, rectal, vaginal, or byinhalation. By “co-administer” it is meant that an RA drug isadministered at the same time, just prior to, or just after theadministration of a second drug (e.g., another RA drug, a drug usefulfor reducing the side-effects of the RA drug, etc.).

A therapeutically effective amount of an RA drug may be administeredrepeatedly, e.g., at least 2, 3, 4, 5, 6, 7, 8, or more times, or thedose may be administered by continuous infusion. The dose may take theform of solid, semi-solid, lyophilized powder, or liquid dosage forms,such as, for example, tablets, pills, pellets, capsules, powders,solutions, suspensions, emulsions, suppositories, retention enemas,creams, ointments, lotions, gels, aerosols, foams, or the like,preferably in unit dosage forms suitable for simple administration ofprecise dosages.

As used herein, the term “unit dosage form” refers to physicallydiscrete units suitable as unitary dosages for human subjects and othermammals, each unit containing a predetermined quantity of an RA drugcalculated to produce the desired onset, tolerability, and/ortherapeutic effects, in association with a suitable pharmaceuticalexcipient (e.g., an ampoule). In addition, more concentrated dosageforms may be prepared, from which the more dilute unit dosage forms maythen be produced. The more concentrated dosage forms thus will containsubstantially more than, e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,or more times the amount of the RA drug.

Methods for preparing such dosage forms are known to those skilled inthe art (see, e.g., REMINGTON'S PHARMACEUTICAL SCIENCES, 18TH ED., MackPublishing Co., Easton, Pa. (1990)). The dosage forms typically includea conventional pharmaceutical carrier or excipient and may additionallyinclude other medicinal agents, carriers, adjuvants, diluents, tissuepermeation enhancers, solubilizers, and the like. Appropriate excipientscan be tailored to the particular dosage form and route ofadministration by methods well known in the art (see, e.g., REMINGTON'SPHARMACEUTICAL SCIENCES, supra).

Examples of suitable excipients include, but are not limited to,lactose, dextrose, sucrose, sorbitol, mannitol, starches, gum acacia,calcium phosphate, alginates, tragacanth, gelatin, calcium silicate,microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water,saline, syrup, methylcellulose, ethylcellulose,hydroxypropylmethylcellulose, and polyacrylic acids such as Carbopols,e.g., Carbopol 941, Carbopol 980, Carbopol 981, etc. The dosage formscan additionally include lubricating agents such as talc, magnesiumstearate, and mineral oil; wetting agents; emulsifying agents;suspending agents; preserving agents such as methyl-, ethyl-, andpropyl-hydroxy-benzoates (i.e., the parabens); pH adjusting agents suchas inorganic and organic acids and bases; sweetening agents; andflavoring agents. The dosage forms may also comprise biodegradablepolymer beads, dextran, and cyclodextrin inclusion complexes.

For oral administration, the therapeutically effective dose can be inthe form of tablets, capsules, emulsions, suspensions, solutions,syrups, sprays, lozenges, powders, and sustained-release formulations.Suitable excipients for oral administration include pharmaceuticalgrades of mannitol, lactose, starch, magnesium stearate, sodiumsaccharine, talcum, cellulose, glucose, gelatin, sucrose, magnesiumcarbonate, and the like.

In some embodiments, the therapeutically effective dose takes the formof a pill, tablet, or capsule, and thus, the dosage form can contain,along with an RA drug, any of the following: a diluent such as lactose,sucrose, dicalcium phosphate, and the like; a disintegrant such asstarch or derivatives thereof; a lubricant such as magnesium stearateand the like; and a binder such a starch, gum acacia,polyvinylpyrrolidone, gelatin, cellulose and derivatives thereof. An RAdrug can also be formulated into a suppository disposed, for example, ina polyethylene glycol (PEG) carrier.

Liquid dosage forms can be prepared by dissolving or dispersing an RAdrug and optionally one or more pharmaceutically acceptable adjuvants ina carrier such as, for example, aqueous saline (e.g., 0.9% w/v sodiumchloride), aqueous dextrose, glycerol, ethanol, and the like, to form asolution or suspension, e.g., for oral, topical, or intravenousadministration. An RA drug can also be formulated into a retentionenema.

For topical administration, the therapeutically effective dose can be inthe form of emulsions, lotions, gels, foams, creams, jellies, solutions,suspensions, ointments, and transdermal patches. For administration byinhalation, an RA drug can be delivered as a dry powder or in liquidform via a nebulizer. For parenteral administration, the therapeuticallyeffective dose can be in the form of sterile injectable solutions andsterile packaged powders. Preferably, injectable solutions areformulated at a pH of from about 4.5 to about 7.5.

The therapeutically effective dose can also be provided in a lyophilizedform. Such dosage forms may include a buffer, e.g., bicarbonate, forreconstitution prior to administration, or the buffer may be included inthe lyophilized dosage form for reconstitution with, e.g., water. Thelyophilized dosage form may further comprise a suitable vasoconstrictor,e.g., epinephrine. The lyophilized dosage form can be provided in asyringe, optionally packaged in combination with the buffer forreconstitution, such that the reconstituted dosage form can beimmediately administered to an individual.

In therapeutic use for the treatment of RA, an RA drug can beadministered at the initial dosage of from about 0.001 mg/kg to about1000 mg/kg daily. A daily dose range of from about 0.01 mg/kg to about500 mg/kg, from about 0.1 mg/kg to about 200 mg/kg, from about 1 mg/kgto about 100 mg/kg, or from about 10 mg/kg to about 50 mg/kg, can beused. The dosages, however, may be varied depending upon therequirements of the individual, the severity of RA symptoms, and the RAdrug being employed. For example, dosages can be empirically determinedconsidering the severity of RA symptoms, the stage of RA, and/or theprognosis of RA in an individual. The dose administered to anindividual, in the context of the present invention, should besufficient to affect a beneficial therapeutic response in the individualover time. The size of the dose can also be determined by the existence,nature, and extent of any adverse side-effects that accompany theadministration of a particular RA drug in an individual. Determinationof the proper dosage for a particular situation is within the skill ofthe practitioner. Generally, treatment is initiated with smaller dosageswhich are less than the optimum dose of the RA drug. Thereafter, thedosage is increased by small increments until the optimum effect undercircumstances is reached. For convenience, the total daily dosage may bedivided and administered in portions during the day, if desired.

As used herein, the term “RA drug” includes all pharmaceuticallyacceptable forms of a drug that is useful for treating one or moresymptoms associated with RA. For example, the RA drug can be in aracemic or isomeric mixture, a solid complex bound to an ion exchangeresin, or the like. In addition, the RA drug can be in a solvated form.The term “RA drug” is also intended to include all pharmaceuticallyacceptable salts, derivatives, and analogs of the RA drug beingdescribed, as well as combinations thereof. For example, thepharmaceutically acceptable salts of an RA drug include, withoutlimitation, the tartrate, succinate, tartarate, bitartarate,dihydrochloride, salicylate, hemisuccinate, citrate, maleate,hydrochloride, carbamate, sulfate, nitrate, and benzoate salt formsthereof, as well as combinations thereof and the like. Any form of an RAdrug is suitable for use in the methods of the present invention, e.g.,a pharmaceutically acceptable salt of an RA drug, a free base of an RAdrug, or a mixture thereof.

Suitable drugs that are useful for treating one or more symptomsassociated with RA include, but are not limited to, disease-modifyinganti-rheumatic drugs (DMARDs), non-steroidal anti-inflammatory drugs(NSAIDs), immunosuppressive drugs, corticosteroids, free bases thereof,pharmaceutically acceptable salts thereof, derivatives thereof, analogsthereof, and combinations thereof.

Non-limiting examples of DMARDs include methotrexate (MTX), leflunomide,D-penicillamine, gold salts (e.g., sodium aurothiomalate, auranofin,etc), minocycline, anti-malarial medications (e.g., chloroquine,hydroxychloroquine, sulfasalazine, etc.), free bases thereof,pharmaceutically acceptable salts thereof, derivatives thereof, analogsthereof, and combinations thereof.

Examples of NSAIDs include, but are not limited to, ibuprofen,indomethacin, COX-2 inhibitors (e.g., Celecoxib), free bases thereof,pharmaceutically acceptable salts thereof, derivatives thereof, analogsthereof, and combinations thereof.

Examples of immunosuppressive drugs include, without limitation,thiopurine drugs such as azathioprine (AZA), 6-mercaptopurine (6-MP),and metabolites thereof (e.g., 6-thioguanine); sirolimus (rapamycin);temsirolimus; everolimus; tacrolimus (FK-506); FK-778; immunosuppressiveantibodies such as anti-tumor necrosis factor (TNF) antibodies (e.g.,adalimumab, infliximab, etc.), anti-lymphocyte globulin antibodies,anti-thymocyte globulin antibodies, anti-CD3 antibodies, anti-CD4antibodies, and antibody-toxin conjugates; cyclosporine; mycophenolate;mizoribine monophosphate; scoparone; glatiramer acetate;cyclophosphamide; IL-1 inhibitors; metabolites thereof; pharmaceuticallyacceptable salts thereof; derivatives thereof; prodrugs thereof; andcombinations thereof.

An individual can also be monitored at periodic time intervals to assessthe efficacy of a certain therapeutic regimen once a diagnosis orprognosis of RA has been made. For example, the presence or level ofcertain RA-associated autoantibodies (e.g., ACPAs and/or RF) may changebased on the therapeutic effect of a treatment such as an RA drug. Incertain embodiments, the patient is monitored to assess response andunderstand the effects of certain RA drugs or treatments in anindividualized approach. In certain other embodiments, patients may notrespond to a drug, but the presence or level of certain RA-associatedautoantibodies may change, indicating that these patients belong to aspecial population (not responsive) that can be identified by theirautoantibody levels. These patients can be discontinued on their currenttherapy and alternative treatments prescribed.

IX. Examples

The present invention will be described in greater detail by way ofspecific examples. The following examples are offered for illustrativepurposes, and are not intended to limit the invention in any manner.Those of skill in the art will readily recognize a variety ofnoncritical parameters which can be changed or modified to yieldessentially the same results.

Example 1 Immunoassay for Detecting Anti-Citrullinated ProteinAntibodies

This example describes an enzyme-linked immunosorbent assay (ELISA) fordetecting (e.g., measuring) the presence (or absence) or level ofanti-citrullinated protein antibodies (ACPAs) in an individual's sample.As a non-limiting example, a 96-well immunoassay plate was coated withavidin (e.g., neutravidin) and the plate was blocked with 5% bovineserum albumin in phosphate buffered saline. Biotinylated syntheticcitrullinated peptides of the present invention were incubated with theavidin-coated plate. After washing, ACPA-positive serum standards orhuman serum samples were added to the plate and incubated for 1 hour atroom temperature. Unbound samples were washed out and RA-associatedautoantibodies directed against the immobilized citrullinated peptidewere detected with an enzyme-labeled (e.g., HRP-labeled) anti-human IgA,IgG, IgM, or IgA/G/M secondary antibody.

Example 2 Design and Application of Novel Citrullinated Peptides

This example describes the design of citrullinated peptide sequencesbased upon human vimentin (SEQ ID NO:1), fibrinogen alpha chain (SEQ IDNO:2), fibrinogen beta chain (SEQ ID NO:3), and alpha-enolase (SEQ IDNO:5) protein sequences. This example also demonstrates the utility ofthe novel citrullinated peptides of the present invention in detectinganti-citrullinated protein antibodies (ACPAs) with improved sensitivityand/or specificity.

Vimentin

The citrullinated peptides shown in Table 1 were designed from thewild-type human vimentin sequence and characterized for their ability tobind to and detect ACPAs.

TABLE 1 Exemplary citrullinated vimentin peptides of thepresent invention. VMT1: Biotin-Gly-Gly-Gly-Ala-Thr-Cit-Ser-Ser-Ala-Val-Arg-Leu-Arg-Ser-Ser-Val-Pro-Gly-Val-Arg-Leu-Leu-Gln-Asp-Ser-NH₂ (SEQ ID NO: 40)VMT2: Biotin-Gly-Gly-Gly-Ala-Thr-Arg-Ser-Ser-Ala-Val-Cit-Leu-Arg-Ser-Ser-Val-Pro-Gly-Val-Arg-Leu-Leu-Gln-Asp-Ser-NH₂ (SEQ ID NO: 42)VMT3: Biotin-Gly-Gly-Gly-Ala-Thr-Arg-Ser-Ser-Ala-Val-Arg-Leu-Cit-Ser-Ser-Val-Pro-Gly-Val-Arg-Leu-Leu-Gln-Asp-Ser-NH₂ (SEQ ID NO: 44)VMT4: Biotin-Gly-Gly-Gly-Ala-Thr-Arg-Ser-Ser-Ala-Val-Arg-Leu-Arg-Ser-Ser-Val-Pro-Gly-Val-Cit-Leu-Leu-Gln-Asp-Ser-NH₂ (SEQ ID NO: 46)VMT5: Biotin-Gly-Gly-Gly-Ala-Thr-Cit-Ser-Ser-Ala-Val-Cit-Leu-Cit-Ser-Ser-Val-Pro-Gly-Val-Cit-Leu-Leu-Gln-Asp-Ser-NH₂ (SEQ ID NO: 48) Each peptide has a biotin coupled atthe N-terminus for binding to the ELISA plate, a glycine (Gly) spacerbetween the biotin moiety and vimentin sequence, and an amide at theC-terminus.

FIG. 2 illustrates dose-response curves for each of these citrullinatedvimentin peptides using an ELISA to detect the presence or absence ofACPAs. FIG. 3 illustrates a comparison of the dose-response curves forthese citrullinated vimentin peptides using an ELISA to detect thepresence or absence of ACPAs. All five of these peptides had peptideepitope scores ≧+2.0 (see, Example 4). As shown in FIG. 3, strongdose-response curves were observed for the VMT2 and VMT3 peptidescompared to the other peptides tested. The weak dose-response curveobserved for the VMT5 peptide may be due to the substitution of all fourarginines with citrullines. This highlights the importance of balancingthe degree of citrullination with antibody recognition such that thepeptide contains a number of citrulline residues that is optimal forimmunological reactivity with ACPAs.

Table 2 shows the affinity of each of these citrullinated vimentinpeptides for IgA, IgG, IgM, or IgA/G/M ACPAs. As illustrated in Table 2,the VMT2 peptide exhibited a particularly high sensitivity forautoantibodies of the IgA and IgM classes, while the VMT3 peptidedisplayed a particularly high sensitivity for autoantibodies of the IgGand IgA/G/M classes. Since IgM and IgA are early markers for rheumatoidarthritis (RA), with IgM being an earlier marker than IgA, the VMT2peptide may be useful for diagnosing an early form of the disease (e.g.,early RA). Since IgG is a late/mature marker for RA, the VMT3 peptide isadvantageous in diagnosing an established or late form of the disease(e.g., erosive RA or destructive RA).

TABLE 2 EC₅₀ of citrullinated vimentin peptides binding to differentautoantibodies. Antibody Binding Affinity of Vimentin Peptides Expressedin EC₅₀ Value Peptides VMT1 VMT2 VMT3 VMT4 VMT5 Auto- IgA 103.6 0.3610.2 34.82 15.6 antibodies IgG 268.7 9.68 3.08 14.33 10.03 IgM 137.52.07 9.79 83.25 21.8 IgA/G/M 11.86 1.98 1.1 5.15 2.96

Fibrinogen Alpha Chain

The citrullinated peptides shown in Table 3 were designed from thewild-type human fibrinogen alpha chain sequence and characterized fortheir ability to bind to and detect ACPAs.

TABLE 3 Exemplary citrullinated fibrinogen alpha chainpeptides of the present invention.α32: Biotin-Gly-Gly-Gly-Pro-Arg-Val-Val-Glu-Arg-His-Gln-Ser-Ala-Gly-Gly-Gly-Thr-Lys-Arg-Gly-His-Ala-Lys-Ser-Arg-Pro-Val-Arg-Gly-Ile-His-Thr (SEQ ID NO: 389)Cit-α32: Biotin-Gly-Gly-Gly-Pro-Cit-Val-Val-Glu-Cit-His-Gln-Ser-Ala-Gly-Gly-Gly-Thr-Lys-Cit-Gly-His-Ala-Lys-Ser-Cit-Pro-Val-Cit-Gly-Ile-His-Thr (SEQ ID NO: 390)[Arg²⁵]Cit-α32: Biotin-Gly-Gly-Gly-Pro-Cit-Val-Val-Glu-Cit-His-Gln-Ser-Ala-Gly-Gly-Gly-Thr-Lys-Cit-Gly-His-Ala-Lys-Ser-Arg-Pro-Val-Cit-Gly-Ile-His-Thr (SEQ ID NO: 391)FB2-α(36-50)^(Cit38,42): Biotin-Gly-Pro-Cit-Val-Val-Glu-Cit-His-Gln-Ser-Ala-Ser-Lys-Asp-Ser-NH₂ (SEQ ID NO: 86)FB4-α(617-631)Cit^(621,630): Biotin-His-Ser-Thr-Lys-Cit-Gly-His-Ala-Lys-Ser-Arg-Pro-Val-Cit-Gly-NH₂ (SEQ ID NO: 88) Each ofthe first three peptides has a biotin coupled at the N-terminus forbinding to the ELISA plate, a glycine (Gly) spacer between theN-terminal and C-terminal portions of the fibrinogen alpha chainsequence, and a carboxylic acid at the C-terminus. Each of the last twopeptides has a biotin coupled at the N-terminus for binding to the ELISAplate and is amidated at the C-terminus. The underlined serine wassubstituted for cysteine present in the wild-type fibrinogen alpha chainsequence.

FIG. 4 illustrates the dose-response curve for the [Arg²⁵]Cit-α32peptide using an ELISA to detect the presence or absence of IgG ACPAs.This peptide was compared to a cyclic citrullinated peptide (CCP) IgGassay available from INOVA Diagnostics, Inc. (San Diego, Calif.). TheEC50 of the INOVA assay was 143-fold higher than the EC₅₀ of the[Arg²⁵]Cit-α32 peptide assay, meaning that the inventive assay is 143times more sensitive than INOVA's CCP assay for detecting IgG ACPAs.FIG. 5 illustrates a comparison of the IgG ACPA values obtained usingthe INOVA CCP assay versus the [Arg²⁵]Cit-α32 peptide assay for normalhuman serum (NHS) and RF-positive (C) samples. FIG. 6 illustrates thedose-response curves for the [Arg²⁵]Cit-α32 peptide using an ELISA todetect the presence or absence of IgA, IgG, IgM, or IgA/G/M ACPAs. Thesefigures show that the [Arg²⁵]Cit-α32 peptide exhibited a particularlyhigh sensitivity for autoantibodies of the IgG class. Since IgG is alate/mature marker for RA, the [Arg²⁵]Cit-α32 peptide is advantageous indiagnosing an established or late form of the disease (e.g., erosive RAor destructive RA).

FIG. 7 illustrates the dose-response curves for additional citrullinatedfibrinogen alpha chain peptides of the invention using an ELISA todetect the presence or absence of ACPAs. The FB4 peptide, which had apeptide epitope score+2.0, showed a stronger dose-response curvecompared to the FB2 peptide, which had a peptide epitope score <+2.0(see, Example 4).

Fibrinogen Beta Chain

The citrullinated peptides shown in Table 4 were designed from thewild-type human fibrinogen beta chain sequence and certain peptides werecharacterized for their ability to bind to and detect ACPAs.

TABLE 4 Exemplary citrullinated fibrinogen beta chainpeptides of the present invention.β32: Biotin-Gly-Gly-Gly-His-Arg-Pro-Leu-Asp-Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Leu-Arg-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Arg-Ala-Arg-CO2HBiotin-Gly-Gly-Gly-His-Arg-Pro-Leu-Asp-Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Leu-Arg-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Arg-Ala-Arg-COOH (SEQ ID NO: 106)Cit-β32: Biotin-Gly-Gly-Gly-His-Cit-Pro-Leu-Asp-Lys-Lys-Cit-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Cit-Ala-Cit- COOH (SEQ ID NO: 108)[Arg¹¹]Cit-β32: Biotin-Gly-Gly-Gly-His-Cit-Pro-Leu-Asp-Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Cit-Ala-Cit-COOH (SEQ ID NO: 110)FB3-β(60-74)^(Cit60,72,74): Biotin-Cit-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Cit-Ala-Cit-NH₂ (SEQ ID NO: 112)FB5-β(43-62)Cit^(47,60): Biotin-Ala-Arg-Gly-His-Cit-Pro-Leu-Asp-Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Pro-Ala-NH₂ (SEQ ID NO: 114) Each of the first three peptides has abiotin coupled at the N-terminus for binding to the ELISA plate, aglycine (Gly) spacer between the biotin moiety and fibrinogen beta chainsequence, and a carboxylic acid at the C-terminus. Each of the last twopeptides has a biotin coupled at the N-terminus for binding to the ELISAplate and is amidated at the C-terminus.

FIG. 7 illustrates the dose-response curves for the FB3 and FB5 peptidesof the invention using an ELISA to detect the presence or absence ofACPAs. The FB3 peptide, which had a peptide epitope score+2.0, showed astronger dose-response curve compared to the FB5 peptide, which had apeptide epitope score <+2.0 (see, Example 4).

Alpha-Enolase

The citrullinated peptides shown in Table 5 were designed from thewild-type human alpha-enolase sequence and characterized for theirability to bind to and detect ACPAs (see, FIG. 25 and Example 7).

TABLE 5 Exemplary citrullinated alpha-enolase peptides ofthe present invention. H-Enls 1: Biotin-Cys-Lys-Ile-His-Ala-Cit-Glu-Ile-Phe-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val-Glu-Cys-NH₂ (SEQ ID NO: 68)H-Enls 2: Biotin-Cys-Lys-Ile-His-Ala-Arg-Glu-Ile-Phe-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val-Glu-Cys-NH₂ (SEQ ID NO: 70)H-Enls 3: Biotin-Ala-Lys-Ile-His-Ala-Arg-Glu-Ile-Phe-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val-Glu-Ala-NH₂ (SEQ ID NO: 72)Pg-Enls 1: Biotin-Cys-Lys-Ile-Ile-Gly-Cit-Glu-Ile-Leu-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val-Glu-Cys- NH₂ (SEQ ID NO: 392)Pg-Enls 2: Biotin-Ala-Lys-Ile-Ile-Gly-Arg-Glu-Ile-Leu-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val-Glu-Ala- NH₂ (SEQ ID NO: 393)Each peptide has a biotin coupled at the N-terminus for binding to theELISA plate, a cysteine (Cys) or alanine (Ala) spacer at each end of thealpha-enolase sequence, and an amide at the C-terminus.

Example 3 Immunoassay for Detecting Rheumatoid Factor (RF)

This example describes an enzyme-linked immunosorbent assay (ELISA) fordetecting (e.g., measuring) the presence (or absence) or level ofrheumatoid factor (RF) in an individual's sample. The assay describedherein uses Protein L having a reporter group attached thereto (e.g.,Protein L labeled with HRP) as a detection agent to detect totalautoantibodies associated with RA, e.g., human IgA, IgG, and IgM. As anon-limiting example, a 96-well immunoassay plate was coated withneutravidin. Biotinylated human IgG Fc fragment was bound to theneutravidin coated plate. Different concentrations of RF standards orpatient serum samples were incubated in the wells coated with IgG Fc.Unbound samples were washed out and bound RF was incubated with ProteinL-labeled with HRP. Unbound Protein L-HRP was washed out, TMB substratewas used to develop the color, and the presence or level of RF in thesample was detected or calculated using an RF standard curve.

FIG. 8 illustrates the dose-response curve for HRP-labeled Protein Lusing an ELISA to detect the presence or absence of RF. This detectionagent was compared to a kit available from Orgentec Diagnostika GmbH(Mainz, Germany), which uses HRP-labeled secondary antibodies directedagainst each of human IgA, IgG, and IgM. The EC₅₀ of the Orgentec assaywas 697-fold higher than the EC₅₀ of the Protein L assay, meaning thatthe inventive assay is 697 times more sensitive than Orgentec's assayfor detecting RF. FIG. 9 illustrates a comparison of the RF valuesobtained using the Orgentec RF assay versus the Protein L assay fornormal human serum (NHS) and RF-positive samples (C). Without beingbound to any particular theory, the inventive RF assay is substantiallymore sensitive than the commercially available Orgentec assay because itrecognizes the Fab region of human IgA, IgG, and IgM autoantibodieswithout interfering with antibody-antigen binding.

Table 6 illustrates the sensitivity and specificity of the RF and ACPAassays of the present invention for normal human serum (Healthy Control)and rheumatoid arthritis serum (RA Patient) samples. As illustrated inTable 6, the RF and ACPA assays each on their own provided an extremelyhigh level of specificity (>92%), but the combinatorial use of bothassays resulted in an even higher level of specificity (>97%). Similareffects were observed with regard to the sensitivity detected for theseassays.

TABLE 6 Sensitivity and specificity of the inventive RF and ACPA assays.Total Specificity Sensitivity Sample Samples Positive (%) (%) RF Healthy40 3.0 92.5 Control RA Patient 53 31 58.5 ACPA Healthy 37 2 94.6 ControlRA Patient 53 26 49.1 RF & ACPA Healthy 36 1 97.2 Control RA Patient 5337 69.8

Example 4 Prediction and Design of Novel Citrullinated Peptides

This example describes an algorithm for predicting RA-specific antigenicpeptide epitopes in proteins present in synovial fluid and the design ofnovel citrullinated peptides based upon one or more predicted antigenicpeptide epitopes. The citrullinated peptides designed using theprediction method described herein are particularly useful for detectingand measuring anti-citrullinated protein antibodies (ACPAs) present inan individual's sample with improved sensitivity and/or specificity,thereby enabling the early detection and/or prognosis of RA.

To induce autoantibody formation against a protein, the protein has tobe first internalized by the antigen presenting cell (APC). Theinternalized protein is then digested into small peptide fragments inthe endosome and loaded onto the major histocompetability complex (MHC)class II molecule in the endoplasmic reticulum. The peptide/MHC complexis then transported to the surface of the APC through the GolgiApparatus for presentation to the helper T cell through contact with theT cell receptor. Once the T cell recognizes the peptide/MHC complex, itwill instruct the B cell to make an antibody that recognizes theantigenic peptide fragment present in the protein.

An MHC class II molecule is composed of two polypeptide chains: anα-chain and β-chain. The overall shape of the molecule looks like a “hotdog bun” with the anti-parallel β-sheets forming the back of the bun andthe two α-helixes, one from the α-chain and the other from the β-chain,forming the two loaves of the bun. An MHC class II molecule binds anantigenic peptide epitope that is composed of only 9 linear amino acidresidues. The MHC molecule binds to the side-chains of the amino acidsat positions P1, P4, P6, and P9 in the 9-residue peptide antigen. Thepeptide antigen backbone also forms H-bonds with some of the MHC proteinresidues to stabilize the overall structure. With the peptide antigenbound to the MHC molecule, the overall shape of the peptide/MHC complexlooks exactly like a hot dog (peptide antigen) in a bun (MHC). The twoends of the bun are open so that it can accommodate a peptide hot dogthat is longer than 9 amino acids. The extra amino acids from thepeptide will just hang out at the two ends of the MHC molecule and notparticipate in the binding and antibody induction.

Table 7 illustrates the MHC Class II molecules associated withrheumatoid arthritis. The α-chain is identical for the three MHC classII alleles. It is only the β-chain that varies between the alleles andimparts the binding specificity to the peptide antigen.

TABLE 7 MHC Class II molecules associated with RA. MHC Class II Allelesα-chain β-chain HLA-DR1 HLA-DRA1*0101 HLA-DRB1*0101 HLA-DR4.1HLA-DRA1*0101 HLA-DRB1*0401 (Dominant Allele) HLA-DR4.4 HLA-DRA1*0101HLA-DRB1*0404

A previous attempt to predict antigenic peptides that bind to thedominant RA HLA-DR4.1 MHC molecule employed side-chain scanning of arecombinant DRB1*0401 MHC molecule with a P1-anchored peptide library todetermine the binding affinity of the test peptides (Hammer et al. J.Exp. Med., 180:2353-2358 (1994)). The determined binding affinity wasthen divided by the binding affinity of a corresponding peptide that wassubstituted with alanine, which has the smallest side chain. If theaffinity constant was better than alanine at that particular position,the score was positive; if the affinity constant was less than alanineat that particular position, the score was negative. A table was thencompiled that gave the score of each of the 19 native amino acids(except cysteine) at positions 2-9 of the antigenic peptide. The peptidescore was the sum of these values. If the 9-residue peptide epitopescore was equal to or greater than +2.0, the epitope was considered tobe an antigenic peptide. However, this prediction method is notparticularly useful for identifying antigenic peptide epitopes anddesigning citrullinated peptides suitable for detecting RA-associatedautoantibodies for at least the following reasons: (1) no values weregiven for amino acids A, D, E, G, H, K, N, P, Q, R, S, and T at the P1position of the peptide, which limits the utility of the table and thisprediction method because scores of the peptide epitopes that begin withany of these amino acids cannot be determined; and (2) the table doesnot have a value for citrulline, the crucial residue in the peptideantigen that is responsible for the induction of autoantibodies in RApatients.

The predictive algorithm of the present invention overcomes thelimitations of Hammer et al. and is especially advantageous because itcan accurately predict the scores of all of the RA antigenic peptideepitopes present in any protein. In certain embodiments, the inventiveprediction method comprises a computer program which employs the peptideside-chain scanning table of Hammer et al., but with modifications inthe P1 column so that all 9 amino acid positions in the peptide epitopeare now used in the calculation. In addition, each of the arginine (R)residues present in the protein was replaced with glutamine (Q) becausethe side-chain binding affinity value for citrulline was not determinedin the Hammer et al. table and the side-chain of citrulline is closelyrelated to glutamine. Cysteine (C) residues present in the nativeprotein sequence are replaced with serine (S). FIG. 10 illustrates anexemplary peptide epitope side-chain scanning table suitable for use inthe prediction and design of novel citrullinated peptides.

FIG. 11 provides an illustration of how the score of a selected9-residue peptide epitope in the vimentin polypeptide wherein anarginine residue was replaced with glutamine to mimic citrullination isdetermined by the RA antigenic peptide prediction program of the presentinvention. From the protein sequence shown in one letter code, thescores of each successive “frame-shifted” 9-residue peptide epitopes inthe boxed peptide fragment and centered around the ⁷¹R (underlined andmutated to Q) were determined by summing up the individual 9-residueside-chain values obtained from the side-chain scanning table set forthin FIG. 10. The highest scoring peptide epitope from the nine successiveframe-shifted epitope sequences was +5.5, which was assigned as thescore for this ⁷¹R residue.

FIG. 12 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in the vimentinsequence, wherein the arginines were replaced with glutamine. The scoresof the calculated 9-residue peptide epitopes containing the argininemutated to glutamine are shown above the corresponding arginine residuein FIG. 12. Those epitope scores that were ≧+2.0 (i.e., higher than 1.9)are underlined in FIG. 12. Such epitopes were used to design antigenicpeptides for detecting autoantibodies in RA samples such as serum.

FIG. 13 illustrates non-limiting examples of synthetic peptides havingcomposite amino acid sequences derived from high scoring vimentin9-residue peptide epitopes (≧+2.0) determined by the RA antigenicpeptide prediction program of the present invention. The scores for eachof the calculated 9-residue peptide epitopes containing the argininemutated to glutamine are shown above the corresponding citrulline (X)residue in FIG. 13. Each synthetic peptide may contain a biotin coupledat the N-terminus for binding to the ELISA plate, an optional amino acidspacer after the biotin moiety, an amide at the C-terminus, and anoptional amino acid spacer before the C-terminal amide. Table 8 belowsets forth these synthetic peptides as shown in FIG. 13 (i.e., withbiotin and linker moieties) and as the core sequence only (see, SEQ IDNOS:50-67).

Referring to FIG. 13, Peptide (1), also known as “VMT6” in Table 8, is a32-mer synthetic peptide containing amino acids 2-13 of human vimentin(SEQ ID NO:1) at the N-terminus, which is linked (i.e., by a peptidebond) to amino acids 4-12 of SEQ ID NO:1, which is linked to amino acids22-31 of SEQ ID NO:1 at the C-terminus, wherein the “X” denotessubstitution of arginine with citrulline. Peptide (2), also known as“VMT7” in Table 8, is a 33-mer synthetic peptide containing amino acids28-38 of SEQ ID NO:1 at the N-terminus, which is linked to amino acids42-52 of SEQ ID NO:1, which is linked to amino acids 61-70 of SEQ IDNO:1 at the C-terminus, wherein the “X” denotes substitution of argininewith citrulline. Peptide (3), also known as “VMT8” in Table 8, is a26-mer synthetic peptide containing amino acids 63-78 of SEQ ID NO:1 atthe N-terminus, which is linked to amino acids 68-76 of SEQ ID NO:1 atthe C-terminus, wherein the “X” denotes substitution of arginine withcitrulline. Peptide (4), also known as “VMT9” in Table 8, is a 27-mersynthetic peptide containing amino acids 96-104 of SEQ ID NO:1 at theN-terminus, which is linked to amino acids 116-124 of SEQ ID NO:1, whichis linked to amino acids 158-165 of SEQ ID NO:1 at the C-terminus,wherein the “X” denotes substitution of arginine with citrulline.Peptide (5), also known as “VMT10” in Table 8, is a 32-mer syntheticpeptide containing amino acids 157-165 of SEQ ID NO:1 at the N-terminus,which is linked to amino acids 205-217 of SEQ ID NO:1, which is linkedto amino acids 216-224 of SEQ ID NO:1 at the C-terminus, wherein the “X”denotes substitution of arginine with citrulline. Peptide (6), alsoknown as “VMT11” in Table 8, is a 21-mer synthetic peptide containingamino acids 266-276 of SEQ ID NO:1 at the N-terminus, which is linked toamino acids 320-328 of SEQ ID NO:1 at the C-terminus, wherein the “X”denotes substitution of arginine with citrulline, and wherein thecysteine at position 328 of SEQ ID NO:1 is replaced with a serine in thecomposite sequence. Peptide (7), also known as “VMT12” in Table 8, is a27-mer synthetic peptide containing amino acids 302-327 of SEQ ID NO:1,wherein the “X” denotes substitution of arginine with citrulline.Peptide (8), also known as “VMT13” in Table 8, is a 31-mer syntheticpeptide containing amino acids 356-364 of SEQ ID NO:1 at the N-terminus,which is linked to amino acids 393-412 of SEQ ID NO:1 at the C-terminus,wherein the “X” denotes substitution of arginine with citrulline.Peptide (9), also known as “VMT14” in Table 8, is a 37-mer syntheticpeptide containing amino acids 417-452 of SEQ ID NO:1, wherein the “X”denotes substitution of arginine with citrulline. One skilled in the artwill appreciate that the synthetic peptides shown in FIG. 13 areexemplary peptides of the present invention, and that other suitable RAantigenic peptides may be designed by linking the antigenic peptideepitope fragments of vimentin in alternative combinations or withantigenic peptide epitopes from other RA-associated polypeptidesdescribed herein (see, e.g., Example 5). As a non-limiting example, thesynthetic peptide may contain one, two, three, four, five, six, or morepeptide epitopes of human vimentin linked by peptide bonds, wherein eachpeptide epitope comprises at least 9 contiguous amino acids of SEQ IDNO:1 and includes at least one arginine residue with a score ≧+2.0 asdetermined by the RA antigenic peptide prediction program describedherein, and wherein the synthetic peptide is immunoreactive againstRA-associated autoantibodies present in an individual's sample.

FIG. 14 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in thefibrinogen alpha chain sequence, wherein the arginines were replacedwith glutamine. The scores of the calculated 9-residue peptide epitopescontaining the arginine mutated to glutamine are shown above thecorresponding arginine residue in FIG. 14. Those epitope scores thatwere ≧+2.0 are underlined in FIG. 14. Such epitopes were used to designantigenic peptides for detecting autoantibodies in RA samples such asserum.

FIG. 15 illustrates non-limiting examples of synthetic peptides havingcomposite amino acid sequences derived from high scoring fibrinogenalpha chain 9-residue peptide epitopes (≧+2.0) determined by the RAantigenic peptide prediction program of the present invention. Thescores for each of the calculated 9-residue peptide epitopes containingthe arginine mutated to glutamine are shown above the correspondingcitrulline (X) residue in FIG. 15. Each synthetic peptide may contain abiotin coupled at the N-terminus for binding to the ELISA plate, anoptional amino acid spacer after the biotin moiety, an amide at theC-terminus, and an optional amino acid spacer before the C-terminalamide. Table 8 below sets forth these synthetic peptides as shown inFIG. 15 (i.e., with biotin and linker moieties) and as the core sequenceonly (see, SEQ ID NOS:90-105).

Referring to FIG. 15, Peptide (1), also known as “Fib-A1” in Table 8, isa 31-mer synthetic peptide containing amino acids 35-43 of humanfibrinogen alpha chain (SEQ ID NO:2) at the N-terminus, which is linked(i.e., by a peptide bond) to amino acids 76-89 of SEQ ID NO:2, which islinked to amino acids 177-183 of SEQ ID NO:2 at the C-terminus, whereinthe “X” denotes substitution of arginine with citrulline, and whereinthe cysteine at position 180 of SEQ ID NO:2 is replaced with a serine inthe composite sequence. Peptide (2), also known as “Fib-A2” in Table 8,is a 31-mer synthetic peptide containing amino acids 107-136 of SEQ IDNO:2, wherein the “X” denotes substitution of arginine with citrulline.Peptide (3), also known as “Fib-A3” in Table 8, is a 32-mer syntheticpeptide containing amino acids 127-148 of SEQ ID NO:2 at the N-terminus,which is linked to amino acids 153-161 of SEQ ID NO:2 at the C-terminus,wherein the “X” denotes substitution of arginine with citrulline.Peptide (4), also known as “Fib-A4” in Table 8, is a 33-mer syntheticpeptide containing amino acids 174-188 of SEQ ID NO:2 at the N-terminus,which is linked to amino acids 213-220 of SEQ ID NO:2, which is linkedto amino acids 212-220 of SEQ ID NO:2 at the C-terminus, wherein the “X”denotes substitution of arginine with citrulline, and wherein thecysteines at positions 180 and 184 of SEQ ID NO:2 are replaced withserines in the composite sequence. Peptide (5), also known as “Fib-A5”in Table 8, is a 32-mer synthetic peptide containing amino acids 393-401of SEQ ID NO:2 at the N-terminus, which is linked to amino acids 359-368of SEQ ID NO:2, which is linked to amino acids 450-460 at theC-terminus, wherein the “X” denotes substitution of arginine withcitrulline. Peptide (6), also known as “Fib-A6” in Table 8, is a 25-mersynthetic peptide containing amino acids 451-465 at the N-terminus,which is linked to amino acids 509-517 at the C-terminus, wherein the“X” denotes substitution of arginine with citrulline, and wherein thecysteine at position 461 of SEQ ID NO:2 is replaced with a serine in thecomposite sequence. Peptide (7), also known as “Fib-A7” in Table 8, is a30-mer synthetic peptide containing amino acids 539-549 at theN-terminus, which is linked to amino acids 583-599 at the C-terminus,wherein the “X” denotes substitution of arginine with citrulline.Peptide (8), also known as “Fib-A8” in Table 8, is a 28-mer syntheticpeptide containing amino acids 613-639 of SEQ ID NO:2, wherein the “X”denotes substitution of arginine with citrulline. One skilled in the artwill appreciate that the synthetic peptides shown in FIG. 15 areexemplary peptides of the present invention, and that other suitable RAantigenic peptides may be designed by linking the antigenic peptideepitope fragments of the fibrinogen alpha chain in alternativecombinations or with antigenic peptide epitopes from other RA-associatedpolypeptides described herein (see, e.g., Example 5). As a non-limitingexample, the synthetic peptide may contain one, two, three, four, five,six, or more peptide epitopes of the human fibrinogen alpha chain linkedby peptide bonds, wherein each peptide epitope comprises at least 9contiguous amino acids of SEQ ID NO:2 and includes at least one arginineresidue with a score ≧+2.0 as determined by the RA antigenic peptideprediction program described herein, and wherein the synthetic peptideis immunoreactive against RA-associated autoantibodies present in anindividual's sample.

FIG. 16 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in thefibrinogen beta chain sequence, wherein the arginines were replaced withglutamine. The scores of the calculated 9-residue peptide epitopescontaining the arginine mutated to glutamine are shown above thecorresponding arginine residue in FIG. 16. Those epitope scores thatwere >+2.0 are underlined in FIG. 16. Such epitopes were used to designantigenic peptides for detecting autoantibodies in RA samples such asserum.

FIG. 17 illustrates non-limiting examples of synthetic peptides havingcomposite amino acid sequences derived from high scoring fibrinogen betachain 9-residue peptide epitopes (≧+2.0) determined by the RA antigenicpeptide prediction program of the present invention. The scores for eachof the calculated 9-residue peptide epitopes containing the argininemutated to glutamine are shown above the corresponding citrulline (X)residue in FIG. 17. Each synthetic peptide may contain a biotin coupledat the N-terminus for binding to the ELISA plate, an optional amino acidspacer after the biotin moiety, an amide at the C-terminus, and anoptional amino acid spacer before the C-terminal amide. Table 8 belowsets forth these synthetic peptides as shown in FIG. 17 (i.e., withbiotin and linker moieties) and as the core sequence only (see, SEQ IDNOS:116-121).

Referring to FIG. 17, Peptide (1), also known as “Fib-B1” in Table 8, isa 32-mer synthetic peptide containing amino acids 70-79 of humanfibrinogen beta chain (SEQ ID NO:3) at the N-terminus, which is linked(i.e., by a peptide bond) to amino acids 150-158 of SEQ ID NO:3, whichis linked to amino acids 188-200 of SEQ ID NO:3 at the C-terminus,wherein the “X” denotes substitution of arginine with citrulline.Peptide (2), also known as “Fib-B2” in Table 8, is a 35-mer syntheticpeptide containing amino acids 192-204 of SEQ ID NO:3 at the N-terminus,which is linked to amino acids 198-207 of SEQ ID NO:3, which is linkedto amino acids 220-230 of SEQ ID NO:3 at the C-terminus, wherein the “X”denotes substitution of arginine with citrulline, and wherein thecysteines at positions 223 and 227 of SEQ ID NO:3 are replaced withserines in the composite sequence. Peptide (3), also known as “Fib-B3”in Table 8, is a 29-mer synthetic peptide containing amino acids 327-336of SEQ ID NO:3 at the N-terminus, which is linked to amino acids 368-376of SEQ ID NO:3, which is linked to amino acids 415-423 of SEQ ID NO:3 atthe C-terminus, wherein the “X” denotes substitution of arginine withcitrulline. One skilled in the art will appreciate that the syntheticpeptides shown in FIG. 17 are exemplary peptides of the presentinvention, and that other suitable RA antigenic peptides may be designedby linking the antigenic peptide epitope fragments of the fibrinogenbeta chain in alternative combinations or with antigenic peptideepitopes from other RA-associated polypeptides described herein (see,e.g., Example 5). As a non-limiting example, the synthetic peptide maycontain one, two, three, four, five, six, or more peptide epitopes ofthe human fibrinogen beta chain linked by peptide bonds, wherein eachpeptide epitope comprises at least 9 contiguous amino acids of SEQ IDNO:3 and includes at least one arginine residue with a score ≧+2.0 asdetermined by the RA antigenic peptide prediction program describedherein, and wherein the synthetic peptide is immunoreactive againstRA-associated autoantibodies present in an individual's sample.

FIG. 18 illustrates the scoring results determined by the RA antigenicpeptide prediction program of the present invention for each of thearginine residues present in a 9-residue peptide epitope in thealpha-enolase sequence, wherein the arginines were replaced withglutamine. The scores of the calculated 9-residue peptide epitopescontaining the arginine mutated to glutamine are shown above thecorresponding arginine residue in FIG. 18. Those epitope scores thatwere ≧+2.0 are underlined in FIG. 18. Such epitopes were used to designantigenic peptides for detecting autoantibodies in RA samples such asserum.

FIG. 19 illustrates non-limiting examples of synthetic peptides havingcomposite amino acid sequences derived from high scoring alpha-enolase9-residue peptide epitopes (≧+2.0) determined by the RA antigenicpeptide prediction program of the present invention. The scores for eachof the calculated 9-residue peptide epitopes containing the argininemutated to glutamine are shown above the corresponding citrulline (X)residue in FIG. 19. Each synthetic peptide may contain a biotin coupledat the N-terminus for binding to the ELISA plate, an optional amino acidspacer after the biotin moiety, an amide at the C-terminus, and anoptional amino acid spacer before the C-terminal amide. Table 8 belowsets forth these synthetic peptides as shown in FIG. 19 (i.e., withbiotin and linker moieties) and as the core sequence only (see, SEQ IDNOS:74-79).

Referring to FIG. 19, Peptide (1), also known as “H-Enls-4” in Table 8,is a 34-mer synthetic peptide containing amino acids 12-22 of humanalpha-enolase (SEQ ID NO:5) at the N-terminus, which is linked (i.e., bya peptide bond) to amino acids 29-40 of SEQ ID NO:5, which is linked toamino acids 47-56 of SEQ ID NO:5 at the C-terminus, wherein the “X”denotes substitution of arginine with citrulline. Peptide (2), alsoknown as “H-Enls-5” in Table 8, is a 33-mer chimeric peptide containingamino acids 130-139 of SEQ ID NO:5 at the N-terminus, which is linked toamino acids 268-279 of SEQ ID NO:5, which is linked to amino acids321-330 of SEQ ID NO:5 at the C-terminus, wherein the “X” denotessubstitution of arginine with citrulline. Peptide (3), also known as“H-Enls-6” in Table 8, is a 33-mer chimeric peptide containing aminoacids 364-376 of SEQ ID NO:5 at the N-terminus, which is linked to aminoacids 411-419 of SEQ ID NO:5, which is linked to amino acids 425-434 ofSEQ ID NO:5 at the C-terminus, wherein the “X” denotes substitution ofarginine with citrulline. One skilled in the art will appreciate thatthe chimeric peptides shown in FIG. 19 are exemplary peptides of thepresent invention, and that other suitable RA antigenic peptides may bedesigned by linking the antigenic peptide epitope fragments ofalpha-enolase in alternative combinations or with antigenic peptideepitopes from other RA-associated polypeptides described herein (see,e.g., Example 5). As a non-limiting example, the synthetic peptide maycontain one, two, three, four, five, six, or more peptide epitopes ofhuman alpha-enolase linked by peptide bonds, wherein each peptideepitope comprises at least 9 contiguous amino acids of SEQ ID NO:5 andincludes at least one arginine residue with a score ≧+2.0 as determinedby the RA antigenic peptide prediction program described herein, andwherein the synthetic peptide is immunoreactive against RA-associatedautoantibodies present in an individual's sample.

In addition to the above-described proteins, any other protein presentin synovial fluid may be analyzed to identify RA antigenic peptideepitopes by applying the prediction program of the present invention.Non-limiting examples of synovial fluid proteins are described inGobezie et al., Arthritis Res. & Ther., 9:R36 (2007). In certainembodiments, structural proteins or enzymes found in synovial fluid maybe citrullinated. Structural proteins are more likely to becitrullinated because they are constantly present in high abundance inthe synovium. Preferably, high scoring (e.g., ≧+2.0) citrullinatedpeptide epitopes from synovial fluid proteins such as collagen, actin,aggrecan, gelsolin, lumican, fibronectin, lamin, myeloblastin, PLscramblase, apolipoprotein (a), BiP, histone, syndecan, CD44, ICAM-I,VCAM-I, glypican, vitronectin, nidogen, tropomyosin, cartilageoligomeric matrix protein, and glucose-6-phosphate isomerase areidentified using the algorithmic prediction program of the presentinvention, and citrullinated peptides based on one or more of theidentified antigenic epitopes are chemically synthesized. In someinstances, individual RA patient serum can be screened with a pool ofsynthetic citrullinated peptides derived from each synovial fluidprotein to detect the presence of RA-associated autoantibodies. In otherinstances, all of the high affinity antigenic citrullinated peptides canbe pooled and used as the antigen in an assay such as an ELISA to detectautoantibodies in patients with early RA.

In some embodiments, the present invention identifies and provides aprofile of the autoantibodies against a particular set of citrullinatedsynovial fluid proteins in a patient sample, wherein the presence ofautoantibodies against one or more of the citrullinated synovial fluidproteins in the set provides information on the stage of RA, therebyenabling the classification of RA patients into different diseasestages, i.e., early stage, middle stage, or late stage. RA is aheterogeneous disease affecting a large population world-wide, and theheterogeneity in RA may be correlated with the presence of differentautoantibodies against different citrullinated synovial fluid proteinsin a patient at a given stage of the disease. As such, classification ofRA patients into different stages or subsets in accordance with thepresent invention enables a clinician to practice “personalizedmedicine” by treating the heterogeneous population of RA patients withthe appropriate medicine or therapy.

Example 5 Calculation of Percent Identity for the Composite Amino AcidSequence of a Synthetic Peptide

In one aspect, the present invention provides a synthetic peptidecomprising two or more synthetic fragments of 5 to 50 amino acids, whicheach have homology to a fragment of 5 to 50 contiguous amino acids of ahuman protein selected from the group consisting of SEQ ID NOS:1 to 39.In certain embodiments, the composite amino acid sequence of thesynthetic fragment will have at least about 80%, 85%, 90%, 95%, or moreidentity to the composite sequence of the corresponding fragments of thehuman protein(s).

In order to calculate the percent identity of the composite sequences,any linker residues should be removed from the amino acid sequence ofthe synthetic peptide to generate the composite amino acid sequence ofthe synthetic fragments. This sequence would then be compared to thecomposite sequence of the corresponding human protein fragments. Forexample, vimentin synthetic peptide (1), shown in FIG. 13, consists ofthree synthetic fragments corresponding to fragments of the humanvimentin protein (SEQ ID NO:1), to which a biotin molecule is attachedto the N-terminus through a glycine linker. After removing the glycinelinker from the synthetic peptide, the composite sequence of thesynthetic fragments is STXSVSSSSYRXRSVSSSSYXSRPSSSXSYV (SEQ ID NO:51),where X is citrulline. The fragments of the human vimentin correspondingto the synthetic peptide consist of residues 2 to 13 (STRSVSSSSYRR; SEQID NO:394), 4 to 12 (RSVSSSSYR; SEQ ID NO:395), and 22 to 31(SRPSSSRSYV; SEQ ID NO:396) of SEQ ID NO:1. Thus, the composite sequenceof the corresponding human protein fragments isSTRSVSSSSYRRRSVSSSSYRSRPSSSRSYV; (SEQ ID NO:397). When the compositesequence of the synthetic fragments is compared to the compositesequence of the corresponding human protein fragments, wherein for thepurposes of the present invention citrulline is considered to beequivalent or identical to arginine, it is seen that the two sequencesare 100% identical.

Likewise, for a variant of vimentin synthetic peptide (1), wherein thevaline residues are substituted with alanines(GSTXSASSSSYRXRSASSSSYXSRPSSSXSYA (SEQ ID NO:398), where X iscitrulline), the composite amino acid sequence of the syntheticfragments is 90.3% identical to the composite sequence of thecorresponding human protein fragments.

Example 6 Exemplary Citrullinated Peptides of the Present Invention

This example provides the amino acid sequences of exemplary syntheticcitrullinated peptides designed in accordance with the RA antigenicpeptide prediction program described in Example 4.

As shown in Table 8, each synthetic peptide may contain a biotin coupledat the N-terminus, an optional amino acid spacer after the biotinmoiety, either an amidated (NH₂) C-terminus or a carboxylic acid (COOH)C-terminus, and an optional amino acid spacer before the C-terminalamide or carboxylic acid. The peptides were designed to incorporate mostof the 9-amino acid citrullinated antigenic epitopes that score higherthan 1.9 in a synovial protein as determined by the prediction programdescribed in Example 4. Depending on the location of the epitopes, eachpeptide comprises either one contiguous amino acid sequence from asynovial protein or fragments from the same protein joined together bypeptide bonds (i.e., to generate a composite amino acid sequence). Thebeginning and ending amino acid of each peptide or fragment is indicatedby a superscript amino acid number that corresponds to that amino acidnumber in the full-length protein sequence. “Cit” represents theoriginal “Arg” amino acid in the native peptide sequence that has beenreplaced by the unnatural amino acid citrulline. The underlined aminoacid “Ser” in a peptide represents replacement of the amino acid “Cys”in the native peptide sequence in order to eliminate the possibility ofdisulfide bond formation. To enhance solubility and/or antibody binding,most peptides have additional amino acids as spacers that are not foundin the native peptide sequence, and these spacer amino acids areitalicized.

TABLE 8Exemplary synthetic citrullinated peptides of the present invention. The left column shows non-limitingexamples of synthetic peptides with biotin and spacer moieties, while the right column shows the coreamino acid sequence for each synthetic peptide. SEQ SEQ ID ID NameBiotinylated Sequence NO: Core Sequence NO: 1. Vimentin Peptides VMT 1Biotin-Gly-Gly-Gly-Ala⁶²-Thr-Cit-Ser-Ser- 40Ala⁶²-Thr-Cit-Ser-Ser-Ala-Val-Arg-Leu- 41Ala-Val-Arg-Leu-Arg-Ser-Ser-Val-Pro-Arg-Ser-Ser-Val-Pro-Gly-Val-Arg-Leu-Leu-Gly-Val-Arg-Leu-Leu-Gln-Asp-Ser⁸³-NH₂ Gln-Asp-Ser⁸³ VMT2Biotin-Gly-Gly-Gly-Ala⁶²-Thr-Arg-Ser-Ser- 42Ala⁶²-Thr-Arg-Ser-Ser-Ala-Val-Cit-Leu- 43Ala-Val-Cit-Leu-Arg-Ser-Ser-Val-Pro-Gly-Arg-Ser-Ser-Val-Pro-Gly-Val-Arg-Leu-Leu-Val-Arg-Leu-Leu-Gln-Asp-Ser⁸³-NH₂ Gln-Asp-Ser⁸³ VMT3Biotin-Gly-Gly-Gly-Ala⁶²-Thr-Arg-Ser-Ser- 44Ala⁶²-Thr-Arg-Ser-Ser-Ala-Val-Arg-Leu- 45Ala-Val-Arg-Leu-Cit-Ser-Ser-Val-Pro-Gly-Cit-Ser-Ser-Val-Pro-Gly-Val-Arg-Leu-Leu-Val-Arg-Leu-Leu-Gln-Asp-Ser⁸³-NH₂ Gln-Asp-Ser⁸³ VMT4Biotin-Gly-Gly-Gly-Ala⁶²-Thr-Arg-Ser-Ser- 46Ala⁶²-Thr-Arg-Ser-Ser-Ala-Val-Arg-Leu- 47Ala-Val-Arg-Leu-Arg-Ser-Ser-Val-Pro-Arg-Ser-Ser-Val-Pro-Gly-Val-Cit-Leu-Leu-Gly-Val-Cit-Leu-Leu-Gln-Asp-Ser⁸³-NH₂ Gln-Asp-Ser⁸³ VMT5Biotin-Gly-Gly-Gly-Ala⁶²-Thr-Cit-Ser-Ser- 48Ala⁶²-Thr-Cit-Ser-Ser-Ala-Val-Cit-Leu-Cit- 49Ala-Val-Cit-Leu-Cit-Ser-Ser-Val-Pro-Gly-Ser-Ser-Val-Pro-Gly-Val-Cit-Leu-Leu-Gln-Val-Cit-Leu-Leu-Gln-Asp-Ser⁸³-NH₂ Asp-Ser⁸³ VMT6Biotin-Gly-Ser²-Thr-Cit-Ser-Val-Ser-Ser- 50Ser²-Thr-Cit-Ser-Val-Ser-Ser-Ser-Ser-Tyr- 51 Ser-Ser-Tyr-Arg-Cit¹³-Arg⁴-Ser-Val-Ser- Arg-Cit ¹³-Arg⁴-Ser-Val-Ser-Ser-Ser-SerSer-Ser-Ser Tyr-Cit ¹²-Ser²²-Arg-Pro-Ser- Tyr-Cit¹²-Ser²²-Arg-Pro-Ser-Ser-Ser-Cit- Ser-Ser-Cit-Ser-Tyr-Val³¹-NH₂Ser-Tyr-Val³¹ VMT7 Biotin-Gly-Arg²⁸-Ser-Tyr-Val-Thr-Thr-Ser- 52Arg²⁸-Ser-Tyr-Val-Thr-Thr-Ser-Thr-Cit- 53Thr-Cit-Thr-Tyr³⁸-Ser⁴²-Ala-Leu-Arg-Pro-Thr-Tyr³⁸-Ser⁴²-Ala-Leu-Arg-Pro-Ser-Thr-Ser-Thr-Ser-Cit-Ser-Leu⁵²-Tyr⁶¹-Ala-Thr-Ser-Cit-Ser-Leu⁵²-Tyr⁶¹-Ala-Thr-Cit-Ser-Cit-Ser-Ser-Ala-Val-Arg-Leu⁷⁰-NH₂ Ser-Ala-Val-Arg-Leu⁷⁰ VMT8Biotin-Gly-Thr⁶³-Arg-Ser-Ser-Ala-Val-Cit- 54Thr⁶³-Arg-Ser-Ser-Ala-Val-Cit-Leu-Arg- 55Leu-Arg-Ser-Ser-Val-Pro-Gly-Val-Cit ⁷⁸- Ser-Ser-Val-Pro-Gly-Val-Cit⁷⁸-Val⁶⁸-Arg- Val⁶⁸-Arg-Leu-Cit-Ser-Ser-Val-Pro-Gly⁷⁶-Leu-Cit-Ser-Ser-Val-Pro-Gly⁷⁶ NH₂ VMT9Biotin-Gly-Phe⁹⁶-Lys-Asn-Thr-Cit-Thr- 56Phe⁹⁶-Lys-Asn-Thr-Cit-Thr-Asn-Glu- 57Asn-Glu-Lys¹⁰⁴-Asn¹¹⁶-Tyr-Ile-Asp-Lys-Lys¹⁰⁴-Asn¹¹⁶-Tyr-Ile-Asp-Lys-Val-Cit-Phe- Val-Cit-Phe-Leu¹²⁴-Cit¹⁵⁸-Arg-Gln-Val- Leu¹²⁴-Cit ¹⁵⁸-Arg-Gln-Val-Asp-Gln-Leu-Asp-Gln-Leu-Thr¹⁶⁵-NH₂ Thr¹⁶⁵ VMT10Biotin-Gly-Leu¹⁵7-Arg-Cit-Gln-Val-Asp- 58Leu¹⁵⁷-Arg-Cit-Gln-Val-Asp-Gln-Leu- 59Gln-Leu-Thr¹⁶⁵-Ser²⁰⁵-Phe-Cit-Gln-Asp-Thr¹⁶⁵-Ser²⁰⁵-Phe-Cit-Gln-Asp-Val-Asp- Val-Asp-Asn-Ala-Ser-Leu-Ala-Cit²¹⁷- Asn-Ala-Ser-Leu-Ala-Cit ²¹⁷-Ala²¹⁶-Arg-Ala²¹⁶-Arg-Leu-Asp-Leu-Glu-Cit-Lys- Leu-Asp-Leu-Glu-Cit-Lys-Val²²⁴Val²²⁴-NH₂ VMT11 Biotin-Gly-Thr²⁶⁶-Ala-Ala-Leu-Cit-Asp- 60Thr²⁶⁶-Ala-Ala-Leu-Cit-Asp-Val-Arg-Gln- 61Val-Arg-Gln-Gln-Tyr²⁷⁶-Arg³²⁰-Cit-Gln-Gln-Tyr²⁷⁶-Arg³²⁰-Cit-Gln-Val-Gln-Ser- Val-Gln-Ser-Leu-Thr-Ser ³²⁸-NH₂Leu-Thr-Ser ³²⁸ VMT12 Biotin-Gly-Ala³⁰²-Asn-Arg-Asn-Asn-Asp- 62Ala³⁰²-Asn-Arg-Asn-Asn-Asp-Ala-Leu-Cit- 63Ala-Leu-Cit-Gln-Ala-Lys-Gln-Glu-Ser-Gln-Ala-Lys-Gln-Glu-Ser-Thr-Glu-Tyr-Cit-Thr-Glu-Tyr-Cit-Arg-Gln-Val-Gln-Ser- Arg-Gln-Val-Gln-Ser-Leu-Thr³²⁷Leu-Thr³²⁷-NH₂ VMT13 Biotin-Gly-Arg-Ala³⁵⁶-Asn-Tyr-Gln-Asp- 64Ala³⁵⁶-Asn-Tyr-Gln-Asp-Thr-Ile-Gly-Cit ³⁶⁴- 65 Thr-Ile-Gly-Cit³⁶⁴-Leu³⁹³-Asp-Ile-Glu-Ile- Leu³⁹³-Asp-Ile-Glu-Ile-Ala-Thr-Tyr-Cit-Ala-Thr-Tyr-Cit-Lys-Leu-Leu-Glu-Gly-Lys-Leu-Leu-Glu-Gly-Glu-Glu-Ser-Cit-Ile-Glu-Glu-Ser-Cit-Ile-Ser⁴¹²-Arg-NH₂ Ser⁴¹² VMT14Biotin-Gly-Asn⁴¹⁷-Phe-Ser-Ser-Leu-Asn- 66Asn⁴¹⁷-Phe-Ser-Ser-Leu-Asn-Leu-Cit-Glu- 67Leu-Cit-Glu-Thr-Asn-Leu-Asp-Ser-Leu-Thr-Asn-Leu-Asp-Ser-Leu-Pro-Leu-Val-Pro-Leu-Val-Asp-Thr-His-Ser-Lys-Cit-Thr-Asp-Thr-His-Ser-Lys-Cit-Thr-Leu-Leu-Ile-Leu-Leu-Ile-Lys-Thr-Val-Glu-Thr-Cit-Asp-Lys-Thr-Val-Glu-Thr-Cit-Asp-Gly⁴⁵² Gly⁴⁵²-NH₂2. Alpha Enolase Peptides (The underlined sequence contains a disulfide bond between the two Cys)H-Enls-1 Biotin- Cys-Lys⁵-Ile-His-Ala-Cit-Glu-Ile- 68Lys⁵-Ile-His-Ala-Cit-Glu-Ile-Phe-Asp-Ser- 69Phe-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val- Cit-Gly-Asn-Pro-Thr-Val-Glu²¹Glu²¹-Cys-NH₂ H-Enls-2 Biotin- Cys-Lys⁵-Ile-His-Ala-Arg-Glu-Ile- 70Lys⁵-Ile-His-Ala-Arg-Glu-Ile-Phe-Asp-Ser- 71Phe-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val- Cit-Gly-Asn-Pro-Thr-Val-Glu²¹

H-Enls-3 Biotin-Ala-Lys⁵-Ile-His-Ala-Arg-Glu-Ile- 72Lys⁵-Ile-His-Ala-Arg-Glu-Ile-Phe-Asp-Ser- 73Phe-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val- Cit-Gly-Asn-Pro-Thr-Val-Glu²¹Glu²¹-Ala-NH₂ H-Enls-4 Biotin-Gly-Phe¹²-Asp-Ser-Cit-Gly-Asn- 74Phe¹²-Asp-Ser-Cit-Gly-Asn-Pro-Thr-Val- 75Pro-Thr-Val-Glu-Val²²-Gly²⁹-Leu-Phe-Cit-Glu-Val²²-Gly²⁹-Leu-Phe-Cit-Ala-Ala-Val-Ala-Ala-Val-Pro-Ser-Gly-Ala-Ser⁴⁰-Leu⁴⁷-Pro-Ser-Gly-Ala-Ser⁴⁰-Leu⁴⁷-Glu-Leu-Cit-Glu-Leu-Cit-Asp-Asn-Asp-Lys-Thr-Arg⁵⁶- Asp-Asn-Asp-Lys-Thr-Arg⁵⁶ NH₂H-Enls-5 Biotin-Gly-Leu¹³⁰-Tyr-Cit-His-Ile-Ala-Asp- 76Leu¹³⁰-Tyr-Cit-His-Ile-Ala-Asp-Leu-Ala- 77Leu-Ala-Gly¹³⁹-Ser²⁶⁸-Cit-Tyr-Ile-Ser-Pro-Gly¹³⁹-Ser²⁶⁸-Cit-Tyr-Ile-Ser-Pro-Asp-Gln-Asp-Gln-Leu-Ala-Asp-Leu²⁷⁹-Thr³²¹-Val-Leu-Ala-Asp-Leu²⁷⁹-Thr³²¹-Val-Thr-Asn-Thr-Asn-Pro-Lys-Cit-Ile-Ala-Lys³³⁰-NH₂ Pro-Lys-Cit-Ile-Ala-Lys³³⁰H-Enls-6 Biotin-Gly-Gly³⁶⁴-Trp-Gly-Val-Met-Val- 78Gly³⁶⁴-Trp-Gly-Val-Met-Val-Ser-His-Cit- 79Ser-His-Cit-Ser-Gly-Glu-Thr³⁷⁶-Leu⁴¹¹-Cit-Ser-Gly-Glu-Thr³⁷⁶-Leu⁴¹¹-Cit-Ile-Glu-Glu-Ile-Glu-Glu-Glu-Leu-Gly-Ser⁴¹⁹-Gly⁴²⁵-Glu-Leu-Gly-Ser⁴¹⁹-Gly⁴²⁵-Arg-Asn-Phe-Arg-Asn-Phe-Cit-Asn-Pro-Leu-Ala-Lys⁴³⁴- Cit-Asn-Pro-Leu-Ala-Lys⁴³⁴ NH₂3. Fibrin Alpha-Chain Peptides α32 Biotin-Gly-Gly-Gly³⁶-Pro-Arg-Val-Val-80 Gly³⁶-Pro-Arg-Val-Val-Glu-Arg-His-Gln- 81Glu-Arg-His-Gln-Ser-Ala⁴⁶-Gly-Gly-Gly-Ser-Ala⁴⁶-Xaa-Thr⁶¹⁹-Lys-Arg-Gly-His-Ala-Thr⁶¹⁹-Lys-Arg-Gly-His-Ala-Lys-Ser-Arg-Lys-Ser-Arg-Pro-Val-Arg-Gly-Ile-His- Pro-Val-Arg-Gly-Ile-His-Thr⁶³⁴-NH₂Thr⁶³⁴ Cit-α32 Biotin-Gly-Gly-Gly³⁶-Pro-Cit-Val-Val-Glu- 82Gly³⁶-Pro-Cit-Val-Val-Glu-Cit-His-Gln- 83Cit-His-Gln-Ser-Ala⁴⁶-Gly-Gly-Gly-Thr⁶¹⁹-Ser-Ala⁴⁶-Xaa-Thr⁶¹⁹-Lys-Cit-Gly-His-Ala-Lys-Cit-Gly-His-Ala-Lys-Ser-Cit-Pro-Val-Lys-Ser-Cit-Pro-Val-Cit-Gly-Ile-His-Thr⁶³⁴ Cit-Gly-Ile-His-Thr⁶³⁴-NH₂[Arg⁶²⁷]Cit- Biotin-Gly-Gly-Gly³⁶-Pro-Cit-Val-Val-Glu- 84Gly³⁶-Pro-Cit-Val-Val-Glu-Cit-His-Gln- 85 α32Cit-His-Gln-Ser-Ala⁴⁶-Gly-Gly-Gly-Thr⁶¹⁹-Ser-Ala⁴⁶-Xaa-Thr⁶¹⁹-Lys-Cit-Gly-His-Ala-Lys-Cit-Gly-His-Ala-Lys-Ser-Arg-Pro-Val-Lys-Ser-Arg-Pro-Val-Cit-Gly-Ile-His-Thr⁶³⁴ Cit-Gly-Ile-His-Thr⁶³⁴-NH₂[Cit^(38,42)]FB2- Biotin-Gly³⁶-Pro-Cit-Val-Val-Glu-Cit-His- 86Gly³⁶-Pro-Cit-Val-Val-Glu-Cit-His-Gln- 87 α(36-50)Gln-Ser-Ala-Ser-Lys-Asp-Ser⁵⁰-NH₂ Ser-Ala-Ser-Lys-Asp-Ser⁵⁰[Cit^(621,630)] Biotin-His⁶¹⁷-Ser-Thr-Lys-Cit-Gly-His-Ala- 88His⁶¹⁷-Ser-Thr-Lys-Cit-Gly-His-Ala-Lys- 89 FB4-α(617-Lys-Ser-Arg-Pro-Val-Cit-Gly⁶³¹-NH₂ Ser-Arg-Pro-Val-Cit-Gly⁶³¹ 631)Fib-A1 Biotin-Gly-Arg³⁵-Gly-Pro-Arg-Val-Val- 90Arg³⁵-Gly-Pro-Arg-Val-Val-Glu-Cit-His⁴³- 91Glu-Cit-His⁴³-Glu⁷⁶-Val-Asn-Gln-Asp-Phe-Glu⁷⁶-Val-Asn-Gln-Asp-Phe-Thr-Asn-Cit-Thr-Asn-Cit-Ile-Asn-Lys-Leu-Lys⁸⁹-Ile¹⁷⁷-Ile-Asn-Lys-Leu-Lys⁸⁹-Ile¹⁷⁷-Arg-Ser-Ser- Arg-Ser-Ser-Cit-Gly-Ser¹⁸³-NH₂Cit-Gly-Ser¹⁸³ Fib-A2 Biotin-Gly-Thr¹⁰⁷-Asn-Ile-Met-Glu-Ile-Leu- 92Thr¹⁰⁷-Asn-Ile-Met-Glu-Ile-Leu-Cit-Gly- 93Cit-Gly-Asp-Phe-Ser-Ser-Ala-Asn-Asn-Asp-Phe-Ser-Ser-Ala-Asn-Asn-Arg-Asp-Arg-Asp-Asn-Thr-Tyr-Asn-Cit-Val-Ser-Asn-Thr-Tyr-Asn-Cit-Val-Ser-Glu-Asp- Glu-Asp-Leu-Arg-Ser¹³⁶-NH₂Leu-Arg-Ser¹³⁶ Fib-A3 Biotin-Gly-Tyr¹²⁷-Asn-Arg-Val-Ser-Glu- 94Tyr¹²⁷-Asn-Arg-Val-Ser-Glu-Asp-Leu-Cit- 95Asp-Leu-Cit-Ser-Arg-Ile-Glu-Val-Leu-Lys-Ser-Arg-Ile-Glu-Val-Leu-Lys-Cit-Lys-Val-Cit-Lys-Val-Ile-Glu-Lys¹⁴⁸-Gln¹⁵³-Leu-Ile-Glu-Lys¹⁴⁸-Gln¹⁵³-Leu-Leu-Gln-Lys-Leu-Gln-Lys-Asn-Val-Cit-Ala¹⁶¹-NH₂ Asn-Val-Cit-Ala¹⁶¹ Fib-A4Biotin-Gly-Asp¹⁷⁴-Ile-Lys-Ile-Cit-Ser-Ser- 96Asp¹⁷⁴-Ile-Lys-Ile-Cit-Ser-Ser-Arg-Gly-Ser- 97Arg-Gly-Ser-Ser-Ser-Cit-Ala-Leu¹⁸⁸-Ser-Ser-Cit-Ala-Leu¹⁸⁸-Leu²¹³-Pro-Ser-Cit-Leu²¹³-Pro-Ser-Cit-Asp-Arg-Gln-His220-Asp-Arg-Gln-His²²⁰-Leu²¹²-Leu-Pro-Ser-Leu²¹²-Leu-Pro-Ser-Arg-Asp-Cit-Gln- Arg-Asp-Cit-Gln-His²²⁰ His²²⁰-NH₂Fib-A5 Biotin-Gly-Arg-Phe³⁹³-Cit-Pro-Asp-Ser- 98Phe³⁹³-Cit-Pro-Asp-Ser-Pro-Gly-Ser-Gly⁴⁰¹- 99Pro-Gly-Ser-Gly⁴⁰¹-Thr³⁵⁹-Trp-Asn-Pro-Thr³⁵⁹-Trp-Asn-Pro-Gly-Ser-Ser-Glu-Cit-Gly-Ser-Ser-Glu-Cit-Gly³⁶⁸-Thr⁴⁴⁰-Ser-Gly-Gly³⁶⁸-Thr⁴⁴⁰-Ser-Gly-Ser-Thr-Thr-Thr-Thr-Ser-Thr-Thr-Thr-Thr-Cit-Arg-Ser⁴⁶⁰-NH₂ Cit-Arg-Ser⁴⁵⁰ Fib-A6Biotin-Gly-Ser⁴⁵¹-Gly-Ser-Thr-Thr-Thr- 100Ser⁴⁵¹-Gly-Ser-Thr-Thr-Thr-Thr-Arg-Cit- 101Thr-Arg-Cit-Ser-Ser-Ser-Lys-Thr-Val⁴⁶⁵-Ser-Ser-Ser-Lys-Thr-Val⁴⁶⁵-Phe⁵⁰⁹-Arg-His-Phe⁵⁰⁹-Arg-His-Cit-His-Pro-Asp-Glu- Cit-His-Pro-Asp-Glu-Ala⁵¹⁷Ala⁵¹⁷-NH₂ Fib-A7 Biotin-Gly-Arg-Glu⁵³⁹-Phe-Val-Ser-Glu- 102Glu⁵³⁹-Phe-Val-Ser-Glu-Thr-Glu-Ser-Cit- 103Thr-Glu-Ser-Cit-Gly-Ser⁵⁴⁹-Phe⁵⁸³-Thr-Ser-Gly-Ser⁵⁴⁹-Phe⁵⁸³-Thr-Ser-Ser-Thr-Ser-Tyr-Ser-Thr-Ser-Tyr-Asn-Cit-Gly-Asp-Ser-Thr-Asn-Cit-Gly-Asp-Ser-Thr-Phe-Glu-Ser- Phe-Glu-Ser-Lys⁵⁹⁹-NH₂ Lys⁵⁹⁹Fib-A8 Biotin-Gly-His⁶¹³-Glu-Gly-Thr-His-Ser- 104His⁶¹³-Glu-Gly-Thr-His-Ser-Thr-Lys-Cit- 105Thr-Lys-Cit-Gly-His-Ala-Lys-Ser-Arg-Pro-Gly-His-Ala-Lys-Ser-Arg-Pro-Val-Cit-Gly-Val-Cit-Gly-Ile-His-Thr-Ser-Pro-Leu-Gly-Ile-His-Thr-Ser-Pro-Leu-Gly-Lys⁶³⁹ Lys⁶³⁹-NH₂4. Fibrin Beta-Chain Peptides β32 Biotin-Gly-Gly-Gly⁴⁵-His-Arg-Pro-Leu-106 Gly⁴⁵-His-Arg-Pro-Leu-Asp-Lys-Lys-Arg- 107Asp-Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Glu-Glu-Ala-Pro-Ser-Leu-Arg-Pro-Ala-Pro-Leu-Arg-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Arg-Ala- Gly-Gly-Tyr-Arg-Ala-Arg⁷⁴-COOHArg⁷⁴ Cit-β32 Biotin-Gly-Gly-Gly⁴⁵-His-Cit-Pro-Leu-Asp- 108Gly⁴⁵-His-Cit-Pro-Leu-Asp-Lys-Lys-Cit- 109Lys-Lys-Cit-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Pro-Ala-Pro-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Cit-Ala- Tyr-Cit-Ala-Cit ⁷⁴-COOH Cit ⁷⁴[Arg⁵³]Cit- Biotin-Gly-Gly-Gly⁴⁵-His-Cit-Pro-Leu-Asp- 110Gly⁴⁵-His-Cit-Pro-Leu-Asp-Lys-Lys-Arg- 111 β32Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Leu-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Pro-Ala-Pro-Cit-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly-Pro-Pro-Ile-Ser-Gly-Gly-Gly-Tyr-Cit-Ala- Gly-Tyr-Cit-Ala-Cit ⁷⁴-COOH Cit⁷⁴ [Cit^(60,72,74)] Biotin-Cit ⁶⁰-Pro-Ala-Pro-Pro-Pro-Ile-Ser- 112 Cit⁶⁰-Pro-Ala-Pro-Pro-Pro-Ile-Ser-Gly-Gly- 113 FB3-β(60-74)Gly-Gly-Gly-Tyr-Cit-Ala-Cit ⁷⁴-NH₂ Gly-Tyr-Cit-Ala-Cit ⁷⁴[Cit^(47,60)]FB5- Biotin-Ala⁴³-Arg-Gly-His-Cit-Pro-Leu- 114Ala⁴³-Arg-Gly-His-Cit-Pro-Leu-Asp-Lys- 115 β(43-62)Asp-Lys-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Lys-Arg-Glu-Glu-Ala-Pro-Ser-Leu-Cit-Pro- Leu-Cit-Pro-Ala⁶²-NH₂ Ala⁶²Fib-B1 Biotin-Gly⁷⁰-Tyr-Arg-Ala-Cit-Pro-Ala-Lys- 116Gly⁷⁰-Tyr-Arg-Ala-Cit-Pro-Ala-Lys-Ala- 117Ala-Ala⁷⁹-Leu¹⁵⁰-Leu-Lys-Asp-Leu-Trp-Ala⁷⁹-Leu¹⁵⁰-Leu-Lys-Asp-Leu-Trp-Gln- Gln-Lys-Cit¹⁵⁸-Asn¹⁸⁸-Ser-Asn-Ile-Pro-Thr- Lys-Cit¹⁵⁸-Asn¹⁸⁸-Ser-Asn-Ile-Pro-Thr-Asn- Asn-Leu-Cit-Val-Leu-Arg-Ser²⁰⁰-NH₂Leu-Cit-Val-Leu-Arg-Ser²⁰⁰ Fib-B2 Biotin-Gly-Pro¹⁹²-Thr-Asn-Leu-Arg-Val-118 Pro¹⁹²-Thr-Asn-Leu-Arg-Val-Leu-Cit-Ser- 119Leu-Cit-Ser-Ile-Leu-Glu-Asn²⁰⁴-Leu¹⁹⁸-Ile-Leu-Glu-Asn²⁰⁴-Leu¹⁹⁸-Arg-Ser-Ile-Leu-Arg-Ser-Ile-Leu-Glu-Asn-Leu-Cit-Ser²⁰⁷-Glu-Asn-Leu-Cit-Ser²⁰⁷-Met²²⁰-Glu-Tyr-Met²²⁰-Glu-Tyr-Ser-Cit-Thr-Pro-Ser-Thr-Ser-Cit-Thr-Pro-Ser-Thr-Val-Ser²³⁰ Val-Ser²³⁰-NH₂ Fib-B3Biotin-Gly-Asp³²⁷-Lys-Ile-Ser-Gln-Leu- 120Asp³²⁷-Lys-Ile-Ser-Gln-Leu-Thr-Cit-Met- 121Thr-Cit-Met-Gly³³⁶-Tyr³⁶⁸-Gln-Ile-Ser-Val-Gly³³⁶-Tyr³⁶⁸-Gln-Ile-Ser-Val-Asn-Lys-Tyr- Asn-Lys-Tyr-Cit³⁷⁶-Trp⁴¹⁵-Leu-Thr-Ser- Cit ³⁷⁶-Trp⁴¹⁵-Leu-Thr-Ser-Asp-Pro-Cit-Lys-Asp-Pro-Cit-Lys-Gln⁴²³-NH₂ Gln⁴²³ 5. Fibrin Gamma-Chain Peptides Fib-G1Biotin-Gly-Tyr²⁷-Val-Ala-Thr-Cit-Asp- 122Tyr²⁷-Val-Ala-Thr-Cit-Asp-Asn-Ser-Ser- 123Asn-Ser-Ser-Ile-Leu-Asp-Glu-Cit-Phe-Gly-Ile-Leu-Asp-Glu-Cit-Phe-Gly-Ser⁴³-Xaa-Ser⁴³-Arg-Ile¹²⁶-Leu-Thr-His-Asp-Ser-Ser-Ile¹²⁶-Leu-Thr-His-Asp-Ser-Ser-Ile-Cit- Ile-Cit-Tyr¹³⁵-Arg-NH₂ Tyr¹³⁵Fib-G2 Biotin-Gly-Val²¹⁹-Phe-Gln-Lys-Cit-Leu- 124Val²¹⁹-Phe-Gln-Lys-Cit-Leu-Asp-Gly-Ser- 125Asp-Gly-Ser-Val-Asp-Phe²³⁰-Tyr³⁰⁰-Cit-Val-Asp-Phe²³⁰-Tyr³⁰⁰-Cit-Leu-Thr-Tyr-Leu-Thr-Tyr-Ala-Tyr-Phe-Ala³⁰⁸-Thr⁴⁰⁹-Ala-Tyr-Phe-Ala³⁰⁸-Thr⁴⁰⁹-Met-Lys-Ile-Ile-Met-Lys-Ile-Ile-Pro-Phe-Asn-Cit-Leu- Pro-Phe-Asn-Cit-Leu-Thr⁴¹⁹Thr⁴¹⁹-Arg-NH₂ 6. Fibronectin Peptides Fibronectin-1 Biotin-Gly-Ser²¹⁵-Leu-Gly-Glu-Gly-Ser- 126 Ser ²¹⁵-Leu-Gly-Glu-Gly-Ser-Gly-Cit-Ile-127 Gly-Cit-Ile-Thr-Ser-Thr-Ser-Arg-Asn²²⁹-Thr-Ser-Thr-Ser-Arg-Asn²²⁹-Gly²²¹-Arg-Ile-Gly²²¹-Arg-Ile-Thr-Ser-Thr-Ser-Cit-Asn²²⁹- Thr-Ser-Thr-Ser-Cit-Asn²²⁹Gly-NH₂ Fibronectin-2 Biotin-Gly²²¹-Arg-Ile-Thr-Ser-Thr-Ser-Arg- 128Gly²²¹-Arg-Ile-Thr-Ser-Thr-Ser-Arg-Asn- 129 Asn-Cit²³⁰-Asp²³³-Gln-Asp-Thr-Arg-Thr- Cit ²³⁰-Asp²³³-Gln-Asp-Thr-Arg-Thr-Ser-Ser-Tyr-Cit ²⁴¹-Ser ²³¹-Asn-Asp-Gln-Asp- Tyr-Cit ²⁴¹-Ser²³¹-Asn-Asp-Gln-Asp-Thr- Thr-Cit-Thr-Ser²³⁹-Gly-NH₂ Cit-Thr-Ser²³⁹Fibronectin-3 Biotin-Gly-Val¹⁰¹³-Leu-Val-Cit-Trp-Thr- 130Val¹⁰¹³-Leu-Val-Cit-Trp-Thr-Pro-Pro- 131Pro-Pro-Arg¹⁰²¹-Leu¹⁰¹⁴-Val-Arg-Trp-Thr-Arg¹⁰²¹-Leu¹⁰¹⁴-Val-Arg-Trp-Thr-Pro-Pro- Pro-Pro-Cit-Ala-Gln¹⁰²³-Gly-NH₂Cit-Ala-Gln¹⁰²³ Fibronectin-4 Biotin-Gly-Tyr¹⁰²⁷-Arg-Leu-Thr-Val-Gly-132 Tyr¹⁰²⁷-Arg-Leu-Thr-Val-Gly-Leu-Thr- 133 Leu-Thr-Cit¹⁰³⁵-Pro¹⁰²⁰-Arg-Ala-Gln-Ile- Cit ¹⁰³⁵-Pro¹⁰²⁰-Arg-Ala-Gln-Ile-Thr-Gly-Thr-Gly-Tyr-Cit-Leu-Thr-Val-Gly-Leu-Tyr-Cit-Leu-Thr-Val-Gly-Leu-Thr-Arg^(l035) Thr-Arg¹⁰³⁵-Gly-NH₂Fibronectin-5 Biotin-Arg-Gly¹¹⁸⁹-Val-Leu-Thr-Val-Ser- 134Gly¹¹⁸⁹-Val-Leu-Thr-Val-Ser-Trp-Glu-Cit- 135Trp-Glu-Cit-Ser-Thr-Thr-Pro-Asp-Ile-Thr-Ser-Thr-Thr-Pro-Asp-Ile-Thr-Gly-Tyr-Cit-Gly-Tyr-Cit-Ile-Thr-Thr-Thr-Pro-Thr- Ile-Thr-Thr-Thr-Pro-Thr-Asn¹²¹⁴Asn¹²¹⁴-Arg-NH₂ Fibronectin-6Biotin-Arg-Ile¹³⁷⁹-Ala-Pro-Cit-Ala-Thr-Ile- 136Ile1379-Ala-Pro-Cit-Ala-Thr-Ile-Thr-Gly¹³⁸⁷- 137Thr-Gly¹³⁸⁷-Pro¹³⁸¹-Arg-Ala-Thr-Ile-Thr-Pro1381-Arg-Ala-Thr-Ile-Thr-Gly-Tyr- Gly-Tyr-Cit¹³⁸⁹-Tyr¹³⁸⁸-Arg-Ile-Cit-His- Cit ¹³⁸⁹-Tyr¹³⁸⁸-Arg-Ile-Cit-His-His-Pro-His-Pro-Glu-His¹³⁹⁶-Gly-NH₂ Glu-His¹³⁹⁶ Fibronectin-7Biotin-Gly-Pro¹⁴⁰¹-Cit-Glu-Asp-Arg-Val- 138Pro¹⁴⁰¹-Cit-Glu-Asp-Arg-Val-Pro-His- 139Pro-His-Ser¹⁴⁰⁹-Pro¹⁴⁰¹-Arg-Glu-Asp-Cit-Ser¹⁴⁰⁹-Pro¹⁴⁰¹-Arg-Glu-Asp-Cit-Val-Pro-Val-Pro-His-Ser-Cit-Asn-Ser-Ile-Thr-Leu-His-Ser-Cit-Asn-Ser-Ile-Thr-Leu-Thr- Thr-Asn¹⁴¹⁷-Gly-NH₂ Asn¹⁴¹⁷Fibronectin-8 Biotin-Arg-Thr¹⁵¹⁷-Val-Tyr-Ala-Val-Thr- 140Thr¹⁵¹⁷-Val-Tyr-Ala-Val-Thr-Gly-Cit-Gly- 141Gly-Cit-Gly-Asp-Ser-Pro-Ala-Ser-Ser-Lys-Asp-Ser-Pro-Ala-Ser-Ser-Lys-Pro-Ile-Ser-Pro-Ile-Ser-Ile-Asn-Tyr-Cit-Thr-Glu-Ile-Ile-Asn-Tyr-Cit-Thr-Glu-Ile-Asp-Lys-Pro- Asp-Lys-Pro-Ser¹⁵⁴⁶-Gly-NH₂Ser¹⁵⁴⁶ Fibronectin-9 Biotin-Arg-Pro¹⁶⁵⁵-Gln-Gly-Gln-Val- 142Pro¹⁶⁵⁵-Gln-Gly-Gln-Val-Ser-Cit-Tyr- 143Ser-Cit-Tyr-Arg-Val-Thr-Tyr-Ser- Arg-Val-Thr-Tyr-Ser-Ser¹⁶⁶⁸-Pro¹⁶⁵⁵-Ser¹⁶⁶⁸-Pro¹⁶⁵⁶-Gln-Gly-Gln-Val-Ser-Gln-Gly-Gln-Val-Ser-Arg-Tyr-Cit-Val-Arg-Tyr-Cit-Val-Thr-Tyr-Ser-Ser¹⁶⁶⁸- Thr-Tyr-Ser-Ser¹⁶⁶⁸ Gly-NH₂Fibronectin- Biotin-Gly-Gly²⁰⁵⁶-Phe-Arg-Cit-Thr- 144Gly²⁰⁵⁶-Phe-Arg-Cit-Thr-Thr-Pro-Pro- 145 10Thr-Pro-Pro-Thr-Thr²⁰⁶⁵-Phe²⁰⁵⁷-Cit-Thr-Thr²⁰⁶⁵-Phe²⁰⁵⁷-Cit-Arg-Thr-Thr-Arg-Thr-Thr-Pro-Pro-Thr-Thr-Ala²⁰⁶⁶- Pro-Pro-Thr-Thr-Ala²⁰⁶⁶ Arg-NH₂Fibronectin- Biotin-Gly-Arg¹⁸¹⁸-Arg-Ala-Cit-Val-Thr- 146Arg¹⁸¹⁸-Arg-Ala-Cit-Val-Thr-Asp-Ala-Thr- 147 11Asp-Ala-Thr-Glu-Thr-Thr-Ile-Thr-Ile-Ser-Glu-Thr-Thr-Ile-Thr-Ile-Ser-Trp-Cit-Thr- Trp-Cit-Thr-Lys¹⁸³⁷-NH₂ Lys¹⁸³⁷Fibronectin- Biotin-Arg-Ala¹⁸⁵¹-Asn-Gly-Gln-Thr-Pro- 148Ala¹⁸⁵¹-Asn-Gly-Gln-Thr-Pro-Ile-Gln-Cit- 149 12Ile-Gln-Cit-Thr-Ile-Lys-Pro-Asp-Val-Cit-Thr-Ile-Lys-Pro-Asp-Val-Cit-Ser-Tyr-Thr-Ser-Tyr-Thr-Ile-Thr-Gly¹⁸⁷²-Arg-NH₂ Ile-Thr-Gly¹⁸⁷² 7. Lamin B1 PeptidesLamin-B1-1 Biotin-Gly-Leu²⁰⁵-Glu-Phe-Cit-Lys-Ser- 150Leu²⁰⁵-Glu-Phe-Cit-Lys-Ser-Met-Tyr-Glu- 151Met-Tyr-Glu-Glu-Glu-Ile-Asn-Glu-Thr-Cit-Glu-Glu-Ile-Asn-Glu-Thr-Cit-Arg-Lys-His-Arg-Lys-His-Glu-Thr-Arg-Leu-Val-Glu²²⁹- Glu-Thr-Arg-Leu-Val-Glu²²⁹ NH₂Lamin-B1-2 Biotin-Gly-Arg²²⁰-Arg-Lys-His-Glu-Thr- 152Arg²²⁰-Arg-Lys-His-Glu-Thr-Cit-Leu-Val- 153Cit-Leu-Val-Glu-Val-Asp-Ser-Gly-Cit- Glu-Val-Asp-Ser-Gly-Cit-Gln²³⁵Gln²³⁵-Gly-NH₂ Lamin-B1-3 Biotin-Ser³⁹⁵-Ser-Cit-Val-Thr-Val-Ser-Arg- 154Ser³⁹⁵-Ser-Cit-Val-Thr-Val-Ser-Arg-Ala- 155Ala-Ser-Ser-Ser-Cit-Ser-Val⁴⁰⁹-Ser⁴⁰⁶-Arg-Ser-Ser-Ser-Cit-Ser-Val⁴⁰⁹-Ser⁴⁰⁶-Arg-Ser-Ser-Val-Arg-Thr-Thr-Cit-Gly-Lys-Cit-Lys-Val-Arg-Thr-Thr-Cit-Gly-Lys-Cit-Lys-Arg-Arg-Val-Asp-Val-Glu-Glu-Ser-Glu⁴²⁵-NH₂ Val-Asp-Val-Glu-Glu-Ser-Glu⁴²⁵Lamin-B1-4 Biotin-Gly-Ser³⁹⁵-Ser-Arg-Val-Thr-Val-Ser- 156Ser³⁹⁵-Ser-Arg-Val-Thr-Val-Ser-Cit-Ala- 157Cit-Ala-Ser-Ser-Ser-Arg-Ser-Val-Cit-Thr-Ser-Ser-Ser-Arg-Ser-Val-Cit-Thr-Thr-Arg- Thr-Arg-Gly-Lys⁴¹⁵-NH₂Gly-Lys⁴¹⁵ Lamin-B1-5 Biotin-Asn⁵³³-Ser-Gln-Gly-Glu-Glu-Val- 158Asn⁵³³-Ser-Gln-Gly-Glu-Glu-Val-Ala-Gln- 159Ala-Gln-Cit-Ser-Thr-Val-Phe-Lys-Thr⁵⁴⁸-Cit-Ser-Thr-Val-Phe-Lys-Thr⁵⁴⁸-Phe⁵⁷⁰-His-Phe⁵⁷⁰-His-Gln-Gln-Gly-Thr-Pro-Cit-Ala-Gln-Gln-Gly-Thr-Pro-Cit-Ala-Ser-Asn-Arg- Ser-Asn-Arg-Ser⁵⁸²-Gly-NH₂Ser⁵⁸² 8. Lamin B2 Peptides Lamin-B2-1Biotin-Lys-Leu¹⁷⁸-Glu-Lys-Glu-Thr-Leu- 160Leu¹⁷⁸-Glu-Lys-Glu-Thr-Leu-Met-Cit-Val- 161Met-Cit-Val-Asp-Leu-Glu-Asn-Arg-Ser ¹⁹²- Asp-Leu-Glu-Asn-Arg-Ser¹⁹²-Met¹⁸⁴-Arg- Met¹⁸⁴-Arg-Val-Asp-Leu-Glu-Asn-Cit-Ser-Val-Asp-Leu-Glu-Asn-Cit-Ser-Gln¹⁹³ Gln¹⁹³-NH₂ Lamin-B2-2Biotin-Glu²¹⁸-Cit-Arg-Leu-Val-Glu-Val- 162Glu²¹⁸-Cit-Arg-Leu-Val-Glu-Val-Asp-Ser- 163Asp-Ser-Ser²²⁷-Arg²¹⁹-Cit-Leu-Val-Glu-Ser²²⁷-Arg²¹⁹-Cit-Leu-Val-Glu-Val-Asp-Val-Asp-Ser-Ser-Cit-Gln-Gln-Glu²³¹-NH₂ Ser-Ser-Cit-Gln-Gln-Glu²³¹Lamin-B2-3 Biotin-Lys³⁸³-Leu-Ser-Pro-Ser-Pro-Ser-Ser- 164Lys³⁸³-Leu-Ser-Pro-Ser-Pro-Ser-Ser-Cit- 165Cit-Val³⁹²-Ser³⁸⁹-Ser-Arg-Val-Thr-Val-Ser-Val³⁹²-Ser³⁸⁹-Ser-Arg-Val-Thr-Val-Ser-Cit-Cit-Ala-Thr-Ser-Ser-Ser-Ser-Gly-Ser⁴⁰⁴-Ala-Thr-Ser-Ser-Ser-Ser-Gly-Ser⁴⁰⁴ NH₂ Lamin-B2-4Biotin-Glu⁵⁵⁰-Glu-Val-Ala-Met-Cit-Thr- 166Glu⁵⁵⁰-Glu-Val-Ala-Met-Cit-Thr-Val-Lys- 167Val-Lys-Lys-Ser-Ser-Val-Met-Cit-Glu-Lys-Ser-Ser-Val-Met-Cit-Glu-Asn-Glu-Asn-Glu-Asn-Gly⁵⁶⁹-Phe⁵⁸⁴-His-Gln-Gln-Asn-Gly⁵⁶⁹-Phe⁵⁸⁴-His-Gln-Gln-Gly-Asp-Gly-Asp-Pro-Cit-Thr-Thr-Ser-Arg⁵⁹⁵-NH₂ Pro-Cit-Thr-Thr-Ser-Arg⁵⁹⁵9. Lamin A/C Peptides Lamin-A/C-1Biotin-Gly-Ser⁵-Gln-Arg-Cit-Ala-Thr-Arg- 168Ser⁵-Gln-Arg-Cit-Ala-Thr-Arg-Ser-Gly¹³- 169 Ser-Gly¹³-Cit⁷-Arg-Ala-Thr-Arg-Ser-Gly- Cit ⁷-Arg-Ala-Thr-Arg-Ser-Gly-Ala-Gln¹⁵-Ala-Gln¹⁵-Arg⁷-Arg-Ala-Thr-Cit-Ser-Gly-Arg⁷-Arg-Ala-Thr-Cit-Ser-Gly-Ala-Gln- Ala-Gln-Ala¹⁶-NH₂ Ala¹⁶Lamin-A/C-2 Biotin-Gly-Ala⁴³-Val-Tyr-Ile-Asp-Cit-Val- 170Ala⁴³-Val-Tyr-Ile-Asp-Cit-Val-Arg-Ser- 171Arg-Ser-Leu⁵²-Ala⁴³-Val-Tyr-Ile-Asp-Arg-Leu⁵²-Ala⁴³-Val-Tyr-Ile-Asp-Arg-Val-Cit-Val-Cit-Ser-Leu-Glu-Thr-Glu-Asn-Ala- Ser-Leu-Glu-Thr-Glu-Asn-Ala-Gly⁵⁸Gly⁵⁸-NH₂ Lamin-A/C-3 Biotin-Gly⁵⁸-Leu-Arg-Leu-Cit-Ile-Thr-Glu- 172Gly⁵⁸-Leu-Arg-Leu-Cit-Ile-Thr-Glu-Ser- 173Ser-Glu-Glu-Val-Val-Ser-Cit-Glu-Val-Ser-Glu-Glu-Val-Val-Ser-Cit-Glu-Val-Ser-Gly- Gly-Ile-Lys⁷⁸-NH₂ Ile-Lys⁷⁸Lamin-A/C-4 Biotin-Thr²¹⁸-Lys-Cit-Arg-His-Glu-Thr- 174Thr²¹⁸-Lys-Cit-Arg-His-Glu-Thr-Arg-Leu- 175Arg-Leu-Val²²⁷-Lys²¹⁹-Arg-Cit-His-Glu-Val²²⁷-Lys²¹⁹-Arg-Cit-His-Glu-Thr-Arg-Thr-Arg-Leu-Val²²⁷-Lys²¹⁹-Arg-Arg-His-Leu-Val²²⁷-Lys²¹⁹-Arg-Arg-His-Glu-Thr-Glu-Thr-Cit-Leu-Val-Glu-Ile-Asp-Asn-Cit-Leu-Val-Glu-Ile-Asp-Asn-Gly-Lys-Gln- Gly-Lys-Gln-Cit-Glu²³⁶-NH₂Cit-Glu²³⁶ Lamin-A/C-5 Biotin-Gln²⁹⁴-Ser-Arg-Ile-Cit-Ile-Asp-Ser- 176Gln²⁹⁴-Ser-Arg-Ile-Cit-Ile-Asp-Ser-Leu-Ser- 177 Leu-Ser-Ala-Gln³⁰⁵-Cit²⁹⁶-Ile-Arg-Ile-Asp- Ala-Gln³⁰⁵-Cit ²⁹⁶-Ile-Arg-Ile-Asp-Ser-Leu-Ser-Leu-Ser-Ala-Gln³⁰⁵-Gly-NH₂ Ser-Ala-Gln³⁰⁵ Lamin-A/C-6Biotin-Glu²⁸⁴-Glu-Arg-Leu-Cit-Leu-Ser- 178Glu²⁸⁴-Glu-Arg-Leu-Cit-Leu-Ser-Pro-Ser- 179Pro-Ser-Pro-Thr-Ser-Gln²⁹⁶-Cit ³⁹⁹-Gly-Arg- Pro-Thr-Ser-Gln²⁹⁶-Cit³⁹⁹-Gly-Arg-Ala-Ser- Ala-Ser-Ser-His-Ser-Ser⁴⁰⁷-Arg³⁹⁹-Gly-Cit-Ser-His-Ser-Ser⁴⁰⁷-Arg³⁹⁹-Gly-Cit-Ala-Ser-Ala-Ser-Ser-His-Ser-Ser⁴⁰⁷-NH₂ Ser-His-Ser-Ser⁴⁰⁷ Lamin-A/C-7Biotin-Gln⁴¹⁰-Gly-Gly-Gly-Ser-Val-Thr- 180Gln⁴¹⁰-Gly-Gly-Gly-Ser-Val-Thr-Lys-Lys- 181Lys-Lys-Cit-Lys-Leu-Glu-Ser-Thr-Glu-Ser-Cit-Lys-Leu-Glu-Ser-Thr-Glu-Ser-Arg- Arg-Ser⁴²⁸-NH₂ Ser⁴²⁸ Lamin-A/C-8Biotin-Lys⁴¹⁸-Arg-Lys-Leu-Glu-Ser-Thr- 182Lys⁴¹⁸-Arg-Lys-Leu-Glu-Ser-Thr-Glu-Ser- 183Glu-Ser-Cit-Ser-Ser-Phe-Ser-Gln-His-Ala-Cit-Ser-Ser-Phe-Ser-Gln-His-Ala-Cit-Thr-Cit-Thr-Ser-Gly-Arg-Val-Ala⁴⁴¹-NH₂ Ser-Gly-Arg-Val-Ala⁴⁴¹ Lamin-A/C-9Biotin-Glu⁵³⁷-Val-Ala-Met-Cit-Lys-Leu- 184Glu⁵³⁷-Val-Ala-Met-Cit-Lys-Leu-Val-Arg- 185Val-Arg-Ser-Val-Thr-Val⁵⁴⁹-Arg⁵⁴¹-Lys-Ser-Val-Thr-Val⁵⁴⁹-Arg⁵⁴¹-Lys-Leu-Val-Leu-Val-Cit-Ser-Val-Thr-Val-Val-Glu- Cit-Ser-Val-Thr-Val-Val-Glu-Asp⁵⁵²Asp⁵⁵²-NH₂ Lamin-A/C-10 Biotin-Gly⁵⁷⁴-Asp-Pro-Ala-Glu-Tyr-Asn- 186Gly⁵⁷⁴-Asp-Pro-Ala-Glu-Tyr-Asn-Leu-Cit- 187Leu-Cit-Ser-Arg-Thr-Val-Leu-Ser ⁵⁸⁸- Ser-Arg-Thr-Val-Leu-Ser⁵⁸⁸-Asn⁵⁸⁰-Leu- Asn⁵⁸⁰-Leu-Arg-Ser-Cit-Thr-Val-Leu-Ser-Arg-Ser-Cit-Thr-Val-Leu-Ser-Gly-Thr⁵⁹⁰ Gly-Thr⁵⁹⁰-NH₂ Lamin-A/C-11Biotin-Ser⁶¹⁹-Val-Thr-Val-Thr-Arg-Ser- 188Ser⁶¹⁹-Val-Thr-Val-Thr-Arg-Ser-Tyr-Cit- 189Tyr-Cit-Ser⁶²⁸-Ala⁶¹⁷-Ser-Ser-Val-Thr-Val-Ser⁶²⁸-Ala⁶¹⁷-Ser-Ser-Val-Thr-Val-Thr-Cit-Thr-Cit-Ser-Tyr-Arg-Ser-Val⁶²⁹-NH₂ Ser-Tyr-Arg-Ser-Val⁶²⁹ Lamin-A/C-12Biotin-Ser⁶³⁶-Phe-Gly-Asp-Asn-Leu-Val- 190Ser⁶³⁶-Phe-Gly-Asp-Asn-Leu-Val-Thr-Cit- 191Thr-Cit-Ser-Tyr-Leu-Leu-Gly-Asn-Ser-Ser-Ser-Tyr-Leu-Leu-Gly-Asn-Ser-Ser-Pro-Cit- Pro-Cit-Thr-Gln-Ser⁶⁵⁷-Gly-NH₂Thr-Gln-Ser⁶⁵⁷ 10. β-Actin Peptide β-Actin-1Biotin-Tyr¹⁸⁸-Leu-Met-Lys-Ile-Leu-Thr- 192Tyr¹⁸⁸-Leu-Met-Lys-Ile-Leu-Thr-Glu-Cit- 193Glu-Cit-Gly-Tyr-Ser-Phe-Thr-Thr-Thr-Ala-Gly-Tyr-Ser-Phe-Thr-Thr-Thr-Ala-Glu-Cit- Glu-Cit-Glu²⁰⁷-NH₂ Glu²⁰⁷11. Myeloblastin Peptides Myeloblastin-Biotin-His³⁷-Ser-Cit-Pro-Tyr-Met-Ala-Ser- 194His³⁷-Ser-Cit-Pro-Tyr-Met-Ala-Ser-Leu- 195 1Leu-Gln-Met-Cit-Gly-Asn-Pro-Gly-Ser-Gln-Met-Cit-Gly-Asn-Pro-Gly-Ser-His⁵⁴ His⁵⁴-NH₂ Myeloblastin-Biotin-His⁷¹-Ser-Leu-Arg-Asp-Ile-Pro-Gln- 196His⁷¹-Ser-Leu-Arg-Asp-Ile-Pro-Gln-Cit- 197 2Cit-Leu-Val-Asn-Val-Val-Leu-Gly-Ala-Leu-Val-Asn-Val-Val-Leu-Gly-Ala-His-His-Asn-Val-Cit-Thr-Gln-Glu-Pro-Thr-Asn-Val-Cit-Thr-Gln-Glu-Pro-Thr-Gln-Gln- Gln-Gln-His⁹⁹-Gly-NH₂ His⁹⁹Myeloblastin- Biotin-Ser²¹⁸-Phe-Val-Ile-Trp-Gly-Ser-Ala- 198Ser²¹⁸-Phe-Val-Ile-Trp-Gly-Ser-Ala-Thr- 199 3Thr-Cit-Leu-Phe-Pro-Asp-Phe-Phe-Thr-Cit-Leu-Phe-Pro-Asp-Phe-Phe-Thr-Cit-Val-Cit-Val-Ala-Leu-Tyr-Val-Asp²⁴¹-NH₂ Ala-Leu-Tyr-Val-Asp²⁴¹ Myeloblastin-Biotin-Gly-Asp²⁴¹-Trp-Ile-Cit-Ser-Thr-Leu- 200Asp²⁴¹-Trp-Ile-Cit-Ser-Thr-Leu-Arg-Arg²⁴⁹- 201 4Arg-Arg²⁴⁹-Asp²⁴¹-Trp-Ile-Arg-Ser-Thr-Asp²⁴¹-Trp-Ile-Arg-Ser-Thr-Leu-Arg-Cit-Leu-Arg-Cit-Val²⁵⁰-Trp²⁴²-Ile-Arg-Ser-Thr-Val²⁵⁰-Trp²⁴²-Ile-Arg-Ser-Thr-Leu-Cit-Arg- Leu-Cit-Arg-Val-Glu²⁵¹-NH₂Val-Glu²⁵¹ 12. PL Scramblase Peptide PLBiotin-Thr¹⁶¹-Leu-Cit-Ile-Ile-Asp-Asn-Met- 202Thr¹⁶¹-Leu-Cit-Ile-Ile-Asp-Asn-Met-Gly- 203 Scramblase-1Gly-Gln-Glu-Val-Ile-Thr-Leu-Glu-Cit-Pro-Gln-Glu-Val-Ile-Thr-Leu-Glu-Cit-Pro-Leu- Leu-Arg-Ser¹⁸¹-Ile¹⁷³-Thr-Leu-Glu-Arg- Arg-Ser ¹⁸¹-Ile¹⁷³-Thr-Leu-Glu-Arg-Pro-Leu-Pro-Leu-Cit-Ser-Ser¹⁸²-NH₂ Cit-Ser-Ser¹⁸²13. Apolipoprotein (a) Peptides Apolipo(a)-1Biotin-Gly-Tyr²⁹-His-Gly-Asp-Gly-Gln- 204Tyr²⁹-His-Gly-Asp-Gly-Gln-Ser-Tyr-Cit- 205Ser-Tyr-Cit-Gly-Thr-Tyr-Ser-Thr-Thr-Val-Gly-Thr-Tyr-Ser-Thr-Thr-Val-Thr-Gly-Cit-Thr-Gly-Cit-Thr-Ser-Gln-Ala⁵¹-Arg-NH₂ Thr-Ser-Gln-Ala⁵¹ Apolipo(a)-2Biotin-Gly-Tyr⁸⁹-Thr-Cit-Asp-Pro-Gly-Val- 206Tyr⁸⁹-Thr-Cit-Asp-Pro-Gly-Val-Arg-Trp⁹⁷- 207Arg-Trp⁹⁷-Tyr⁸⁹-Thr-Arg-Asp-Pro-Gly-Val-Tyr⁸⁹-Thr-Arg-Asp-Pro-Gly-Val-Cit-Trp⁹⁷-Cit-Trp⁹⁷-Ser¹²⁸-Glu-Gln-Ala-Pro-Thr-Glu-Ser¹²⁸-Glu-Gln-Ala-Pro-Thr-Glu-Gln-Cit ¹³⁶ Gln-Cit ¹³⁶-Gly-NH₂Apolipo(a)-3 Biotin-Tyr³⁵⁶³-Tyr-His-Tyr-Gly-Gln-Ser- 208Tyr³⁵⁶³-Tyr-His-Tyr-Gly-Gln-Ser-Tyr-Cit- 209Tyr-Cit-Gly³⁵⁷²-Ser³⁶⁸⁷-Phe-Ser-Thr-Thr-Gly³⁵⁷²-Ser³⁶⁸⁷-Phe-Ser-Thr-Thr-Val-Thr-Val-Thr-Gly-Cit-Thr-Ser-Gln-Ser³⁶⁹⁹-Arg- Gly-Cit-Thr-Ser-Gln-Ser³⁶⁹⁹ NH₂Apolipo(a)-4 Biotin-His³⁷⁰⁶-Trp-His-Gln-Cit-Thr-Thr- 210His³⁷⁰⁶-Trp-His-Gln-Cit-Thr-Thr-Glu-Tyr- 211Glu-Tyr-Tyr-Pro-Asn-Gly-Gly-Leu-Thr- Tyr-Pro-Asn-Gly-Gly-Leu-Thr-Cit³⁷²²- Cit ³⁷²²-Gly³⁷¹⁸-Gly-Leu-Thr-Arg-Asn-Tyr-Gly³⁷¹⁸-Gly-Leu-Thr-Arg-Asn-Tyr-Ser-Cit- Ser-Cit-Asn³⁷²⁷-NH₂ Asn³⁷²⁷Apolipo(a)-5 Biotin-Gly-Tyr³⁸⁹⁷-Arg-Gly-Asp-Gly-Gln- 212Tyr³⁸⁹⁷-Arg-Gly-Asp-Gly-Gln-Ser-Tyr-Cit- 213Ser-Tyr-Cit-Gly-Thr-Leu-Ser-Thr-Thr-Ile-Gly-Thr-Leu-Ser-Thr-Thr-Ile-Thr-Gly-Cit-Thr-Gly-Cit-Thr-Ser-Gln-Ser³⁹¹⁹-Arg-NH₂ Thr-Ser-Gln-Ser³⁹¹⁹ Apolipo(a)-6Biotin-His³⁹²⁶-Trp-His-Arg-Cit-Ile-Pro- 214His³⁹²⁶-Trp-His-Arg-Cit-Ile-Pro-Leu-Tyr- 215Leu-Tyr-Tyr-Pro-Asn-Ala-Gly-Leu-Thr- Tyr-Pro-Asn-Ala-Gly-Leu-Thr-Cit³⁹⁴²- Cit ³⁹⁴²-Ala³⁹³⁸-Gly-Leu-Thr-Arg-Asn-Tyr-Ala³⁹³⁸-Gly-Leu-Thr-Arg-Asn-Tyr-Ser-Cit- Ser-Cit-Asn³⁹⁴⁷-NH₂ Asn³⁹⁴⁷Apolipo(a)-7 Biotin-Gly-Tyr⁴⁰¹¹-His-Gly-Asp-Gly-Arg- 216Tyr⁴⁰¹¹-His-Gly-Asp-Gly-Arg-Ser-Tyr-Cit- 217Ser-Tyr-Cit-Gly-Ile-Ser-Ser-Thr-Thr-Val-Gly-Ile-Ser-Ser-Thr-Thr-Val-Thr-Gly-Cit-Thr-Gly-Cit-Thr-Ser-Gln-Ser⁴⁰³³-Arg-NH₂ Thr-Ser-Gln-Ser⁴⁰³³ Apolipo(a)-8Biotin-Ser⁴¹³¹-Tyr-Cit-Gly-Thr-Phe-Ser- 218Ser⁴¹³¹-Tyr-Cit-Gly-Thr-Phe-Ser-Thr-Thr- 219Thr-Thr-Val-Thr-Gly-Cit-Thr-Ser-Gln-Ser-Val-Thr-Gly-Cit-Thr-Ser-Gln-Ser-Trp-Ser-Trp-Ser-Ser-Met-Thr-Pro-His-Cit-His⁴¹⁵⁶-Ser-Met-Thr-Pro-His-Cit-His⁴¹⁵⁶-Arg⁴¹⁵⁵-Arg⁴¹⁵⁵-His-Gln-Cit-Thr-Pro-Glu-Asn⁴¹⁶²- His-Gln-Cit-Thr-Pro-Glu-Asn⁴¹⁶²Gly-NH₂ Apolipo(a)-9 Biotin-Gly-Gly⁴⁵²⁹-Val-Tyr-Ala-Arg-Val- 220Gly⁴⁵²⁹-Val-Tyr-Ala-Arg-Val-Ser-Cit-Phe- 221Ser-Cit-Phe-Val-Thr-Trp-Ile⁴⁵⁴¹-Val⁴⁵³⁰-Val-Thr-Trp-Ile⁴⁵⁴¹-Val⁴⁵³⁰-Tyr-Ala-Cit-Tyr-Ala-Cit-Val-Ser-Arg-Phe-Val-Thr⁴⁵³9- Val-Ser-Arg-Phe-Val-Thr⁴⁵³⁹ NH₂14. BiP Peptides BiP-1 Biotin-Arg-Tyr¹⁷⁵-Phe-Asn-Asp-Ala-Gln- 222Tyr¹⁷⁵-Phe-Asn-Asp-Ala-Gln-Cit-Gln- 223Cit-Gln-Ala¹⁸³-Ile¹⁹⁰-Ala-Gly-Leu-Asn-Ala¹⁸³-Ile¹⁹⁰-Ala-Gly-Leu-Asn-Val-Met-Cit-Val-Met-Cit-Ile-Ile-Asn-Glu-Pro-Thr²⁰³- Ile-Ile-Asn-Glu-Pro-Thr²⁰³Arg-NH₂ BiP-2 Biotin-Asp²⁷⁷-Val-Arg-Lys-Asp-Asn-Cit- 224Asp²⁷⁷-Val-Arg-Lys-Asp-Asn-Cit-Ala-Val- 225Ala-Val-Gln-Lys-Leu-Arg-Cit-Glu-Val-Gln-Lys-Leu-Arg-Cit-Glu-Val-Glu-Lys-Glu-Lys-Ala-Lys-Cit-Ala-Leu-Ser-Ser-Gln-Ala-Lys-Cit-Ala-Leu-Ser-Ser-Gln-His- His-Gln³⁰⁴-NH₂ Gln³⁰⁴ BiP-3Biotin-Gly³¹⁵-Glu-Asp-Phe-Ser-Glu-Thr- 226Gly³¹⁵-Glu-Asp-Phe-Ser-Glu-Thr-Leu-Thr- 227 Leu-Thr-Cit³²⁴-Asp³³³-Leu-Phe-Cit-Ser- Cit ³²⁴-Asp³³³-Leu-Phe-Cit-Ser-Thr-Met-Thr-Met-Lys-Pro³⁴¹-Ile³⁵⁹-Val-Leu-Val-Lys-Pro³⁴¹-Ile³⁵⁹-Val-Leu-Val-Gly-Gly-Ser- Gly-Gly-Ser-Thr-Cit³⁶⁷-Arg-NH₂ Thr-Cit ³⁶⁷ BiP-4 Biotin-Lys⁴³⁵-Leu-Ile-Pro-Cit-Asn-Thr-Val-228 Lys⁴³⁵-Leu-Ile-Pro-Cit-Asn-Thr-Val-Val- 229Val-Pro⁴⁴⁴-Ile⁵²⁴-Thr-Ile-Thr-Asn-Asp-Gln-Pro⁴⁴⁴-Ile⁵²⁴-Thr-Ile-Thr-Asn-Asp-Gln-Asn- Asn-Cit-Leu-Thr⁵³⁴-Arg-NH₂Cit-Leu-Thr⁵³⁴ 15. Histone Peptides Histone H2A-1Biotin-Gly-Leu⁶⁴-Glu-Leu-Ala-Gly-Asn- 230Leu⁶⁴-Glu-Leu-Ala-Gly-Asn-Ala-Ala-Cit- 231Ala-Ala-Cit-Asp-Asn-Lys-Lys-Thr-Arg-Ile-Asp-Asn-Lys-Lys-Thr-Arg-Ile-Ile-Pro-Cit-Ile-Pro-Cit-His-Leu-Gln⁸⁵-Gly-NH₂ His-Leu-Gln⁸⁵ Histone H2B-1Biotin-Ser-Lys³¹-Arg-Ser-Cit-Lys-Glu-Ser- 232Lys³¹-Arg-Ser-Cit-Lys-Glu-Ser-Tyr-Ser- 233Tyr-Ser-Val-Tyr-Val-Tyr-Lys⁴⁴-NH₂ Val-Tyr-Val-Tyr-Lys⁴⁴ Histone H2B-2Biotin-Ser⁶⁵-Phe-Val-Asn-Asp-Ile-Phe-Glu- 234Ser⁶⁵-Phe-Val-Asn-Asp-Ile-Phe-Glu-Cit-Ile- 235Cit-Ile-Ala-Gly-Glu-Ala-Ser-Cit-Leu-Ala-Ala-Gly-Glu-Ala-Ser-Cit-Leu-Ala-His-Tyr-His-Tyr-Asn-Lys-Arg-Ser-Thr-Ile-Thr-Ser-Asn-Lys-Arg-Ser-Thr-Ile-Thr-Ser-Cit-Glu⁹⁴ Cit-Glu⁹⁴-Gly-NH₂Histone H2B-3 Biotin-Ser⁷⁹-Arg-Leu-Ala-His-Tyr-Asn- 236Ser⁷⁹-Arg-Leu-Ala-His-Tyr-Asn-Lys-Cit- 237Lys-Cit-Ser-Thr-Ile-Thr-Ser-Arg-Glu-Ile-Ser-Thr-Ile-Thr-Ser-Arg-Glu-Ile-Gln-Thr-Gln-Thr-Ala-Val-Cit-Leu¹⁰¹-Gly-NH₂ Ala-Val-Cit-Leu¹⁰¹ Histone H3-1Biotin-Arg⁴¹-Tyr-Arg-Pro-Gly-Thr-Val- 238Arg⁴¹-Tyr-Arg-Pro-Gly-Thr-Val-Ala-Leu- 239Ala-Leu-Cit-Glu-Ile-Cit-Arg-Tyr-Gln-Lys-Cit-Glu-Ile-Cit-Arg-Tyr-Gln-Lys-Ser-Thr-Ser-Thr-Glu-Leu-Leu-Ile-Cit-Lys-Leu-Pro-Glu-Leu-Leu-Ile-Cit-Lys-Leu-Pro-Phe-Gln- Phe-Gln-Arg⁷⁰-NH₂ Arg⁷⁰Histone H3-2 Biotin-Asp⁷⁸-Phe-Lys-Thr-Asp-Leu-Cit- 240Asp⁷⁸-Phe-Lys-Thr-Asp-Leu-Cit-Phe-Gln- 241Phe-Gln-Ser-Ser-Ala-Val-Met⁹¹-Ala¹²⁸-Arg-Ser-Ser-Ala-Val-Met⁹¹-Ala¹²⁸-Arg-Arg-Ile-Arg-Ile-Arg-Gly-Glu-Cit-Ala¹³⁶-Gly-NH₂ Arg-Gly-Glu-Cit-Ala¹³⁶Histone H4-1 Biotin-Arg²⁰-Lys-Val-Leu-Cit-Asp-Asn-Ile- 242Arg²⁰-Lys-Val-Leu-Cit-Asp-Asn-Ile-Gln- 243Gln-Gly²⁹-Lys⁹²-Arg-Gln-Gly-Cit-Thr-Leu-Gly²⁹-Lys⁹²-Arg-Gln-Gly-Cit-Thr-Leu-Tyr- Tyr-Gly¹⁰⁰-Gly-NH₂ Gly¹⁰⁰Histone H4-2 Biotin-Gly⁴⁹-Leu-Ile-Tyr-Glu-Glu-Thr-Cit- 244Gly⁴⁹-Leu-Ile-Tyr-Glu-Glu-Thr-Cit-Gly- 245Gly-Val-Leu-Lys-Val-Phe-Leu-Glu-Asn-Val-Leu-Lys-Val-Phe-Leu-Glu-Asn-Val-Ile-Val-Ile-Cit-Asp-Ala-Val-Thr-Tyr-Thr-Glu-Cit-Asp-Ala-Val-Thr-Tyr-Thr-Glu-His-Ala-His-Ala-Lys-Cit-Lys-Thr-Val-Thr-Ala⁸⁴- Lys-Cit-Lys-Thr-Val-Thr-Ala⁸⁴Gly-NH₂ 16. Collagen Peptides Coll. T2α1-1Biotin-Arg-Asn¹²⁶³-Asn-Gln-Ile-Glu-Ser- 246Asn¹²⁶³-Asn-Gln-Ile-Glu-Ser-Ile-Cit-Ser¹²⁷¹- 247Ile-Cit-Ser¹²⁷¹-Ala¹³⁷¹-Asn-Val-Gln-Met-Ala¹³⁷¹-Asn-Val-Gln-Met-Thr-Phe-Leu-Cit-Thr-Phe-Leu-Cit-Leu-Leu-Ser-Thr-Glu- Leu-Leu-Ser-Thr-Glu-Gly-Ser¹³⁸⁶Gly-Ser¹³⁸⁶-Lys-NH₂ Coll. T2α1-2 Biotin-Glu¹⁴²⁰-Ile-Cit-Ala-Glu-Gly-Asn-248 Glu¹⁴²⁰-Ile-Cit-Ala-Glu-Gly-Asn-Ser-Arg- 249Ser-Arg-Phe¹⁴²⁹-Ile¹⁴²¹-Arg-Ala-Glu-Gly-Phe¹⁴²⁹-Ile¹⁴²¹-Arg-Ala-Glu-Gly-Asn-Ser-Asn-Ser-Cit-Phe-Thr-Tyr-Thr-Ala-Leu-Cit-Phe-Thr-Tyr-Thr-Ala-Leu-Lys-Asp¹⁴³⁶ Lys-Asp¹⁴³⁶-NH₂ Coll. T2α1-3Biotin-Lys¹⁴⁴⁴-Trp-Gly-Lys-Thr-Val-Ile- 250Lys¹⁴⁴⁴-Trp-Gly-Lys-Thr-Val-Ile-Glu-Tyr- 251Glu-Tyr-Cit-Ser-Gln-Lys-Thr-Ser-Arg-Cit-Ser-Gln-Lys-Thr-Ser-Arg-Leu¹⁴⁶⁰-Leu¹⁴⁶⁰-Tyr¹⁴⁵²-Arg-Ser-Gln-Lys-Thr-Ser-Tyr¹⁴⁵²-Arg-Ser-Gln-Lys-Thr-Ser-Cit- Cit-Leu¹⁴⁶⁰-Gly-NH₂ Leu¹⁴⁶⁰Coll. T9α1-1 Biotin-Lys²⁶-Arg-Arg-Pro-Cit-Phe-Pro-Val- 252Lys²⁶-Arg-Arg-Pro-Cit-Phe-Pro-Val-Asn- 253Asn-Ser³⁵-Phe⁶³-Gln-Val-Asp-Lys-Ala-Ala-Ser³⁵-Phe⁶³-Gln-Val-Asp-Lys-Ala-Ala-Ser- Ser-Cit⁷¹-Ala⁷³-Ile-Gln-Arg-Val-Val-Gly- Cit⁷¹-Ala⁷³-Ile-Gln-Arg-Val-Val-Gly-Ser⁸⁰-Ser⁸⁰-Arg⁷²-Ala-Ile-Gln-Cit-Val-Val-Gly-Arg⁷²-Ala-Ile-Gln-Cit-Val-Val-Gly-Ser- Ser-Ala⁸¹-NH₂ Ala⁸¹ Coll. T9α1-2Biotin-Gly-Arg⁹⁶-Ile-Pro-Thr-Cit-Asn-Leu- 254Arg⁹⁶-Ile-Pro-Thr-Cit-Asn-Leu-Tyr-Pro¹⁰⁴- 255Tyr-Pro¹⁰⁴-Tyr¹¹¹-Ser-Phe-Leu-Thr-Thr-Tyr¹¹¹-Ser-Phe-Leu-Thr-Thr-Phe-Cit-Met-Phe-Cit-Met-Thr-Gly-Ser-Thr-Leu-Lys- Thr-Gly-Ser-Thr-Leu-Lys-Lys¹²⁶Lys¹²⁶-NH₂ Coll. T9α1-3 Biotin-Gly-His¹⁸¹-Lys-Ile-Met-Ile-Gly-Val- 256His¹⁸¹-Lys-Ile-Met-Ile-Gly-Val-Glu-Cit- 257Glu-Cit-Ser-Ser-Ala-Thr-Leu-Phe-Val-Asp-Ser-Ser-Ala-Thr-Leu-Phe-Val-Asp-Ser-Asn-Ser-Asn-Cit-Ile-Glu-Ser-Leu-Pro-Ile- Cit-Ile-Glu-Ser-Leu-Pro-Ile-Lys²⁰⁷Lys²⁰⁷-NH₂ Coll. T9α1-4 Biotin-Gln⁷⁶⁰-His-Ile-Lys-Gln-Val-Ser-Met- 258Gln⁷⁶⁰-His-Ile-Lys-Gln-Val-Ser-Met-Cit- 259Cit-Val-Ile-Gln-Glu-His-Phe-Ala-Glu-Met-Val-Ile-Gln-Glu-His-Phe-Ala-Glu-Met-Ala- Ala-Ala-Ser-Leu-Lys-Cit⁷⁸³-Gly-NH₂ Ala-Ser-Leu-Lys-Cit ⁷⁸³ Coll. T10α1-1Biotin-Lys⁵²⁷-Ala-Gly-Gln-Cit-Pro-Ser- 260Lys⁵²⁷-Ala-Gly-Gln-Cit-Pro-Ser-Leu-Ser- 261Leu-Ser-Gly⁵³⁶-Asp⁵⁷²-Lys-Ile-Leu-Tyr-Gly⁵³⁶-Asp⁵⁷²-Lys-Ile-Leu-Tyr-Asn-Cit- Asn-Cit-Gln-Gln⁵⁸⁰-Cit⁵⁸⁵-Thr-Gly-Ile-Phe- Gln-Gln⁵⁸⁰-Cit ⁵⁸⁵-Thr-Gly-Ile-Phe-Thr-Ser-Thr-Ser-Gln-Ile⁵⁹³-Arg-NH₂ Gln-Ile⁵⁹³ Coll. T11α1-1 Biotin-Gly-Ser⁶¹-Thr-Asn-Cit-Lys-Asn-Ser- 262 Ser ⁶¹-Thr-Asn-Cit-Lys-Asn-Ser-Lys-Gly-263 Lys-Gly-Ser-Asp-Thr-Ala-Tyr-Cit-Val-Ser-Ser-Asp-Thr-Ala-Tyr-Cit-Val-Ser-Lys-Gln- Lys-Gln-Ala-Gln-Leu-Ser⁸³-NH₂Ala-Gln-Leu-Ser⁸³ Coll. T11α1-2 Biotin-Asp¹⁵⁰-Tyr-Pro-Leu-Phe-Cit-Thr-264 Asp¹⁵⁰-Tyr-Pro-Leu-Phe-Cit-Thr-Val-Asn- 265Val-Asn-Ile-Ala-Asp-Gly-Lys-Trp-His-Cit-Ile-Ala-Asp-Gly-Lys-Trp-His-Cit-Val-Ala-Val-Ala-Ile-Ser-Val-Glu-Lys-Lys¹⁷⁴-Gly- Ile-Ser-Val-Glu-Lys-Lys¹⁷⁴ NH₂Coll. T11α1-3 Biotin-Thr¹⁸⁷-Lys-Pro-Leu-Asp-Cit-Ser- 266Thr¹⁸⁷-Lys-Pro-Leu-Asp-Cit-Ser-Glu-Arg- 267Glu-Arg-Ala¹⁹⁶-Lys¹⁸⁸-Pro-Leu-Asp-Arg-Ala¹⁹⁶-Lys¹⁸⁸-Pro-Leu-Asp-Arg-Ser-Glu- Ser-Glu-Cit-Ala¹⁹⁶-Cit¹⁵⁵⁵-Arg-His-Thr- Cit-Ala¹⁹⁶-Cit ¹⁵⁵⁵-Arg-His-Thr-Glu-Gly-Glu-Gly-Met-Gln-Ala-Asp¹⁵⁶⁴-NH₂ Met-Gln-Ala-Asp¹⁵⁶⁴ Coll. T11α2-1Biotin-Gly⁵²-Ile-Ser-Pro-Ala-Asp-Val-Ala- 268Gly⁵²-Ile-Ser-Pro-Ala-Asp-Val-Ala-Tyr-Cit- 269Tyr-Cit-Val-Ala-Arg-Pro-Ala-Gln-Leu⁶⁸-Val-Ala-Arg-Pro-Ala-Gln-Leu⁶⁸-Tyr⁶⁰-Arg-Tyr⁶⁰-Arg-Val-Ala-Cit-Pro-Ala-Gln-Leu-Val-Ala-Cit-Pro-Ala-Gln-Leu-Ser-Ala-Pro-Ser-Ala-Pro-Thr-Cit-Gln⁷⁴-Arg-NH₂ Thr-Cit-Gln⁷⁴ Coll. T11α2-2Biotin-Lys⁸²-Asp-Phe-Ser-Leu-Leu-Thr- 270Lys⁸²-Asp-Phe-Ser-Leu-Leu-Thr-Val-Val- 271Val-Val-Cit-Thr⁹²-Ser⁸⁵-Leu-Leu-Thr-Val-Cit-Thr⁹²-Ser⁸⁵-Leu-Leu-Thr-Val-Val-Arg-Val-Arg-Thr-Cit-Pro-Gly-Leu-Gln-Ala⁹⁸- Thr-Cit-Pro-Gly-Leu-Gln-Ala⁹⁸Gly-NH₂ Coll. T11α2-3 Biotin-Asn²³⁸-Gln-Gln-Pro-His-Arg-Ala- 272Asn²³⁸-Gln-Gln-Pro-His-Arg-Ala-Gln-Cit- 273Gln-Cit-Ser-Pro-Gln-Gln-Gln-Pro-Ser-Arg-Ser-Pro-Gln-Gln-Gln-Pro-Ser-Arg-Leu-His-Leu-His-Cit-Pro-Gln-Asn-Gln-Glu²⁶²-NH₂ Cit-Pro-Gln-Asn-Gln-Glu²⁶²Coll. T11α2-4 Biotin-Gly-His²⁴²-Cit-Ala-Gln-Arg-Ser- 274His²⁴²-Cit-Ala-Gln-Arg-Ser-Pro-Gln-Gln- 275Pro-Gln-Gln-Gln-Pro-Ser-Cit-Leu-His-Arg-Gln-Pro-Ser-Cit-Leu-His-Arg-Pro-Gln-Asn- Pro-Gln-Asn-Gln-Glu²⁶²-NH₂Gln-Glu²⁶² 17. Syndecan Peptides Syndecan-I-1Biotin-Gly-Pro¹²³-Arg-Pro-Cit-Glu-Thr- 276Pro¹²³-Arg-Pro-Cit-Glu-Thr-Thr-Gln- 277Thr-Gln-Leu¹³¹-Gly¹⁸³-Gly-Pro-Ser-Ala-Leu¹³¹-Gly¹⁸³-Gly-Pro-Ser-Ala-Thr-Glu-Cit- Thr-Glu-Cit-Ala¹⁹¹-Gly-NH₂Ala¹⁹¹ Syndecan-I-2 Biotin-Gly-Val²²⁵-Glu-Pro-Asp-Arg-Cit- 278Val²²⁵-Glu-Pro-Asp-Arg-Cit-Asn-Gln-Ser- 279Asn-Gln-Ser-Pro-Val-Asp-Gln-Gly²³⁸- Pro-Val-Asp-Gln-Gly²³⁸-Cit²²⁹-Arg-Asn- Cit ²²⁹-Arg-Asn-Gln-Ser-Pro-Val-Asp-Gln-Gln-Ser-Pro-Val-Asp-Gln-Gly²³⁸ Gly²³⁸-NH₂ Syndecan-Biotin-Arg-Ser⁹¹-Gly-Ile-Glu-Thr-Ala-Met- 280Ser⁹¹-Gly-Ile-Glu-Thr-Ala-Met-Cit-Phe⁹⁹- 281 III-1Cit-Phe⁹⁹-Glu¹⁴⁷-Val-Pro-Glu-Glu-Pro-Ser-Glu¹⁴⁷-Val-Pro-Glu-Glu-Pro-Ser-Gln-Cit-Gln-Cit-Ala-Thr-Thr-Val-Ser-Thr¹⁶¹-Ala²²²-Ala-Thr-Thr-Val-Ser-Thr¹⁶¹-Ala²²²-Cit- Cit-Ala²²⁴-Arg-NH₂ Ala²²⁴Syndecan- Biotin-Arg-Phe¹⁹⁶-Thr-Ala-Thr-Thr-Ala- 282Phe¹⁹⁶-Thr-Ala-Thr-Thr-Ala-Val-Ile-Cit- 283 III-2Val-Ile-Cit-Thr-Thr-Gly-Val-Arg²⁰⁹-Ala²⁰¹-Thr-Thr-Gly-Val-Arg²⁰⁹-Ala²⁰¹-Val-Ile-Arg-Val-Ile-Arg-Thr-Thr-Gly-Val-Cit-Arg-Thr-Thr-Gly-Val-Cit-Arg-Leu²¹¹-Val²⁰²-Ile-Leu²¹¹-Val²⁰²-Ile-Arg-Thr-Thr-Gly-Val-Arg-Thr-Thr-Gly-Val-Arg-Cit-Leu²¹¹ Arg-Cit-Leu²¹¹-Gly-NH₂ Syndecan-Biotin-Arg-Pro²⁴⁶-Cit-Leu-Val-Ser-Thr- 284Pro²⁴⁶-Cit-Leu-Val-Ser-Thr-Ala-Thr-Ser- 285 III-3Ala-Thr-Ser-Cit-Pro-Arg-Ala-Leu-Pro-Cit-Cit-Pro-Arg-Ala-Leu-Pro-Cit-Pro-Ala-Thr-Pro-Ala-Thr-Thr-Gln-Glu-Pro-Asp-Ile-Pro-Thr-Gln-Glu-Pro-Asp-Ile-Pro-Glu-Cit- Glu-Cit-Ser²⁷⁴-Gly-NH₂ Ser²⁷⁴18. CD44 Peptides CD44-1 Biotin-Arg-Ile²²-Asp-Leu-Asn-Ile-Thr-Ser- 286Ile²²-Asp-Leu-Asn-Ile-Thr-Ser-Cit-Phe-Ala- 287Cit-Phe-Ala-Gly-Val-Phe-His-Val-Glu-Gly-Val-Phe-His-Val-Glu-Lys-Asn-Gly-Lys-Asn-Gly-Cit-Tyr⁴²-Gly⁴⁰-Arg-Tyr-Ser-Cit-Tyr⁴²-Gly⁴⁰-Arg-Tyr-Ser-Ile-Ser-Cit-Ile-Ser-Cit-Thr-Glu-Ala-Ala⁵⁰-Gly-NH₂ Thr-Glu-Ala-Ala⁵⁰ CD44-2Biotin-Arg-Ile⁷²-Gly-Phe-Glu-Thr-Ser-Cit- 288Ile⁷²-Gly-Phe-Glu-Thr-Ser-Cit-Tyr-Gly- 289Tyr-Gly-Phe-Ile-Glu-Gly-His-Val-Val-Ile-Phe-Ile-Glu-Gly-His-Val-Val-Ile-Pro-Cit-Pro-Cit-Ile-His-Pro-Asn-Ser-Ile-Ser ⁹⁷-Arg- Ile-His-Pro-Asn-Ser-Ile-Ser⁹⁷ NH₂ CD44-3 Biotin-Arg-Pro¹⁴²-Ile-Thr-Ile-Thr-Ile-Val- 290Pro¹⁴²-Ile-Thr-Ile-Thr-Ile-Val-Asn-Cit-Asp- 291Asn-Cit-Asp-Gly-Thr-Arg-Tyr-Val¹⁵⁶-Gly-Thr-Arg-Tyr-Val¹⁵⁶-Asn¹⁴⁹-Arg-Asp-Asn¹⁴⁹-Arg-Asp-Gly-Thr-Cit-Tyr-Val¹⁵⁶- Gly-Thr-Cit-Tyr-Val¹⁵⁶ Gly-NH₂CD44-4 Biotin-Gly-Ser¹⁷⁹-Ser-Gly-Ser-Ser-Ser-Glu- 292Ser¹⁷⁹-Ser-Gly-Ser-Ser-Ser-Glu-Cit-Ser¹⁸⁷- 293Cit-Ser¹⁸⁷-Trp²¹¹-Ile-Thr-Asp-Ser-Thr-Asp-Trp²¹¹-Ile-Thr-Asp-Ser-Thr-Asp-Cit-Ile-Cit-Ile-Pro-Ala-Thr-Thr-Leu-Met-Ser²²⁶- Pro-Ala-Thr-Thr-Leu-Met-Ser²²⁶Gly-NH₂ CD44-5 Biotin-Arg-Ser³⁰⁶-Thr-Ile-Ser-Thr-Thr-Pro- 294Ser³⁰⁶-Thr-Ile-Ser-Thr-Thr-Pro-Cit-Ala³¹⁴- 295Cit-Ala³¹⁴-Glu³³⁵-Val-Leu-Leu-Gln-Thr-Glu³³⁵-Val-Leu-Leu-Gln-Thr-Thr-Thr-Cit-Thr-Thr-Cit-Met-Thr³⁴⁵-Arg³⁴³-Met-Thr-Met-Thr³⁴⁵-Arg³⁴³-Met-Thr-Asp-Val-Asp- Asp-Val-Asp-Cit-Asn³⁵⁰-Gly-NH₂Cit-Asn³⁵⁰ CD44-6 Biotin-Gly⁴¹¹-Tyr-Arg-Gln-Thr-Pro-Cit- 296Gly⁴¹¹-Tyr-Arg-Gln-Thr-Pro-Cit-Glu-Asp- 297Glu-Asp-Ser⁴²⁰-Met⁴³⁷-Gln-Gly-Cit-Thr-Ser⁴²⁰-Met⁴³⁷-Gln-Gly-Cit-Thr-Thr-Pro-Ser- Thr-Pro-Ser-Pro⁴⁴⁵-Cit⁴⁶⁹-Arg-Met-Asp- Pro⁴⁴⁵-Cit ⁴⁶⁹-Arg-Met-Asp-Met-Asp-Ser-Met-Asp-Ser-Ser-His⁴⁷⁷-Arg⁴⁶⁹-Cit-Met-Ser-His⁴⁷⁷-Arg⁴⁶⁹-Cit-Met-Asp-Met-Asp-Asp-Met-Asp-Ser-Ser-His⁴⁷⁷-Gly-NH₂ Ser-Ser-His⁴⁷⁷ CD44-7Biotin-Gly-Ser⁵³⁰-Thr-Leu-Thr-Ser-Ser- 298Ser⁵³⁰-Thr-Leu-Thr-Ser-Ser-Asn-Cit-Asn⁵³⁸- 299Asn-Cit-Asn⁵³⁸-Arg⁵³⁷-Asn-Asp-Val-Thr-Arg⁵³⁷-Asn-Asp-Val-Thr-Gly-Gly-Cit ⁵⁴⁴- Gly-Gly-Cit⁵⁴⁴-Gly⁵⁴³-Arg-Cit-Asp-Pro- Gly⁵⁴³-Arg-Cit-Asp-Pro-Asn-His-Ser-Glu⁵⁵¹Asn-His-Ser-Glu⁵⁵¹-Gly-NH₂ CD44-8 Biotin-Arg-Asp⁵⁹³-Ser-Asn-Ser-Asn-Val-300 Asp⁵⁹³-Ser-Asn-Ser-Asn-Val-Asn-Cit-Ser- 301Asn-Cit-Ser-Leu-Ser-Gly⁶⁰⁴-Pro⁶⁴¹-Ile-Cit-Leu-Ser-Gly⁶⁰⁴-Pro⁶⁴¹-Ile-Cit-Thr-Pro-Gln- Thr-Pro-Gln-Ile⁶⁴⁷-Arg-NH₂Ile⁶⁴⁷ 19. ICAM-I Peptides ICAM-I-1Biotin-Arg-Gly¹⁴⁰-Ala-Pro-Cit-Ala-Asn- 302Gly¹⁴⁰-Ala-Pro-Cit-Ala-Asn-Leu-Thr-Val- 303 Leu-Thr-Val-Val-Leu-Leu-Cit¹⁵²-Leu¹⁵¹- Val-Leu-Leu-Cit ¹⁵²-Leu¹⁵¹-Arg-Gly-Glu-Arg-Gly-Glu-Lys-Glu-Leu-Lys-Cit ¹⁵⁹-Gly- Lys-Glu-Leu-Lys-Cit ¹⁵⁹ NH₂ICAM-I-2 Biotin-Gly-Glu¹⁶⁸-Val-Thr-Thr-Thr-Val- 304Glu¹⁶⁸-Val-Thr-Thr-Thr-Val-Leu-Val-Cit- 305Leu-Val-Cit-Arg-Asp-His¹⁷⁹-Gly¹⁸¹-Ala-Arg-Asp-His¹⁷⁹-Gly¹⁸¹-Ala-Asn-Phe-Ser- Asn-Phe-Ser-Ser-Cit-Thr¹⁸⁸-Ser¹⁸⁶-Arg- Ser-Cit-Thr¹⁸⁸-Ser ¹⁸⁶-Arg-Thr-Glu-Leu-Thr-Glu-Leu-Asp-Leu-Cit-Pro¹⁹⁴-Gly-NH₂ Asp-Leu-Cit-Pro¹⁹⁴ ICAM-I-3Biotin-Gly-Leu⁴⁵⁶-Ser-Arg-Ala-Cit-Ser- 306Leu⁴⁵⁶-Ser-Arg-Ala-Cit-Ser-Thr-Gln-Gly- 307Thr-Gln-Gly-Glu-Val-Thr-Cit-Lys-Val-Glu-Val-Thr-Cit-Lys-Val-Thr-Val-Asn-Val-Thr-Val-Asn-Val-Leu-Ser-Pro-Cit-Tyr- Leu-Ser-Pro-Cit-Tyr-Glu⁴⁸⁰Glu⁴⁸⁰-Gly-NH₂ 20. VCAM-I Peptide VCAM-I-1Biotin-Gly-Pro⁴⁹⁶-Lys-Gln-Cit-Gln-Ser- 308Pro⁴⁹⁶-Lys-Gln-Cit-Gln-Ser-Thr-Gln-Thr- 309Thr-Gln-Thr-Leu-Tyr-Val-Asn-Val-Ala-Leu-Tyr-Val-Asn-Val-Ala-Pro-Cit-Asp-Pro-Cit-Asp-Thr-Thr-Val-Leu-Val-Ser- Thr-Thr-Val-Leu-Val-Ser-Pro⁵²⁰Pro⁵²⁰-Arg-NH₂ 21. Glypican Peptides Glypican-I-1Biotin-Gly-Thr⁸⁷-Ala-Leu-Cit-Asp-Ser-Ser- 310Thr⁸⁷-Ala-Leu-Cit-Asp-Ser-Ser-Arg-Val⁹⁵- 311Arg-Val⁹⁵-Ala⁸⁸-Leu-Arg-Asp-Ser-Ser-Cit-Ala⁸⁸-Leu-Arg-Asp-Ser-Ser-Cit-Val-Leu-Val-Leu-Gln-Ala-Met-Leu-Ala-Thr-Gln-Gln-Ala-Met-Leu-Ala-Thr-Gln-Leu-Cit- Leu-Cit-Ser¹⁰⁶-Arg-NH₂ Ser¹⁰⁶Glypican-I-2 Biotin-Gly¹³¹-Glu-Leu-Tyr-Thr-Gln-Asn- 312Gly¹³¹-Glu-Leu-Tyr-Thr-Gln-Asn-Ala-Cit- 313Ala-Cit-Ala¹⁴⁰-Arg¹³⁹-Ala-Phe-Cit-Asp-Ala¹⁴⁰-Arg¹³⁹-Ala-Phe-Cit-Asp-Leu-Tyr-Leu-Tyr-Ser¹⁴⁶-Phe¹⁴¹-Arg-Asp-Leu-Tyr-Ser¹⁴⁶-Phe¹⁴¹-Arg-Asp-Leu-Tyr-Ser-Glu-Ser-Glu-Leu-Cit-Leu-Tyr-Tyr-Cit-Gly-Ala-Leu-Cit-Leu-Tyr-Tyr-Cit-Gly-Ala-Asn- Asn-Leu-His¹⁵⁸-Gly-NH₂ Leu-His¹⁵⁸Glypican-I-3 Biotin-Gly-Leu²¹¹-Arg-Ala-Thr-Cit-Ala- 314Leu²¹¹-Arg-Ala-Thr-Cit-Ala-Phe-Val- 315Phe-Val-Ala²¹⁹-Leu²⁰⁹-Arg-Leu-Cit-Ala-Ala²¹⁹-Leu²⁰⁹-Arg-Leu-Cit-Ala-Thr-Arg-Thr-Arg-Ala-Phe-Val-Ala-Ala-Cit-Ser-Phe-Ala-Phe-Val-Ala-Ala-Cit-Ser-Phe-Val- Val-Gln²²⁵-Gly-NH₂ Gln²²⁵Glypican-I-4 Biotin-Arg-Leu²²⁷-Gly-Val-Ala-Ser-Asp- 316Leu²²⁷-Gly-Val-Ala-Ser-Asp-Val-Val-Cit- 317Val-Val-Cit-Lys-Val-Ala-Gln-Val-Pro-Leu-Lys-Val-Ala-Gln-Val-Pro-Leu-Gly-Pro-Glu-Gly-Pro-Glu-Ser-Ser-Cit-Ala-Val²⁵⁰-Arg- Ser-Ser-Cit-Ala-Val²⁵⁰ NH₂Glypican-I-5 Biotin-Gly-Gln⁴⁵⁹-Leu-Lys-Ile-Met-Thr- 318Gln⁴⁵⁹-Leu-Lys-Ile-Met-Thr-Asn-Cit-Leu- 319Asn-Cit-Leu-Arg-Ser⁴⁶⁹-Leu⁴⁶⁰-Lys-Ile-Arg-Ser⁴⁶⁹-Leu⁴⁶⁰-Lys-Ile-Met-Thr-Asn-Met-Thr-Asn-Arg-Leu-Cit-Ser-Ala-Tyr- Arg-Leu-Cit-Ser-Ala-Tyr-Asn-Gly⁴⁷³Asn-Gly⁴⁷³-Arg-NH₂ Glypican-I-6 Biotin-Gly-Ser ⁴⁹⁹-Gly-Arg-Lys-Val-Ser-320 Ser ⁴⁹⁹-Gly-Arg-Lys-Val-Ser-Cit-Lys-Ser- 321Cit-Lys-Ser-Ser-Ser-Ser-Arg-Thr⁵¹²-Ser⁵⁰⁴-Ser-Ser-Ser-Arg-Thr⁵¹²-Ser⁵⁰⁴-Arg-Lys-Ser-Arg-Lys-Ser-Ser-Ser-Ser-Cit-Thr⁵¹²-Gly- Ser-Ser-Ser-Cit-Thr⁵¹² NH₂Glypican- Biotin-Gly-Ser ⁶⁸-Ser-Ser-Ser-Glu-Thr-Glu- 322 Ser⁶⁸-Ser-Ser-Ser-Glu-Thr-Glu-Gln-Cit ⁷⁶- 323 II-1 Gln-Cit⁷⁶-Arg⁷⁶-Leu-Ile-Cit-Glu-Thr-Glu- Arg⁷⁶-Leu-Ile-Cit-Glu-Thr-Glu-Ala-Thr-Ala-Thr-Phe-Cit-Gly⁸⁷-Arg-NH₂ Phe-Cit-Gly⁸⁷ Glypican-Biotin-Arg²¹²-Leu-Cit-Leu-Gln-Ile-Thr- 324Arg²¹²-Leu-Cit-Leu-Gln-Ile-Thr-Arg-Thr- 325 II-2Arg-Thr-Leu-Val-Ala-Ala-Cit-Ala-Phe-Leu-Val-Ala-Ala-Cit-Ala-Phe-Val-Gln²²⁹-Val-Gln²²⁹-Leu²¹³-Arg-Leu-Gln-Ile-Thr-Leu²¹³-Arg-Leu-Gln-Ile-Thr-Cit-Thr-Leu- Cit-Thr-Leu-Val-Ala²²³-Arg-NH₂Val-Ala²²³ Glypican- Biotin-Arg-Gln²⁷³-Gly-Phe-Ser-Leu-Asn- 326Gln²⁷³-Gly-Phe-Ser-Leu-Asn-Val-Val-Cit- 327 II-3Val-Val-Cit-Gly-Ser-Leu-Ser-Ser-Arg- Gly-Ser-Leu-Ser-Ser-Arg-Gly²⁸⁸-Ser²⁸³-Leu- Gly²⁸⁸-Ser ²⁸³-Leu-Ser-Ser-Cit-Gly²⁸⁸-Gly- Ser-Ser-Cit-Gly²⁸⁸NH₂ Glypican- Biotin-Gly-Pro³⁵¹-Val-Pro-Ala-Cit-Asn- 328Pro³⁵¹-Val-Pro-Ala-Cit-Asn-Arg-Arg- 329 II-4Arg-Arg-Ala³⁵⁹-Pro³⁵¹-Val-Pro-Ala-Arg-Ala³⁵⁹-Pro³⁵¹-Val-Pro-Ala-Arg-Asn-Cit-Asn-Cit-Arg-Ala³⁵⁹-Pro³⁵¹-Val-Pro-Ala-Arg-Ala³⁵⁹-Pro³⁵¹-Val-Pro-Ala-Arg-Asn- Arg-Asn-Arg-Cit-Ala³⁵⁹-Gly-NH₂Arg-Cit-Ala³⁵⁹ Glypican- Biotin-Arg-Ser⁴⁶¹-Gly-Pro-Asp-Val-Pro- 330Ser⁴⁶¹-Gly-Pro-Asp-Val-Pro-Thr-Arg-Cit- 331 II-5Thr-Arg-Cit-Arg⁴⁷⁰-Arg⁴⁷⁰-Cit-Leu-Gln-Arg⁴⁷⁰-Arg⁴⁷⁰-Cit-Leu-Gln-Leu-Arg-Ala-Leu-Arg-Ala-Ala-Thr-Ala-Cit-Met-Lys⁴⁸²- Ala-Thr-Ala-Cit-Met-Lys⁴⁸² NH₂Glypican- Biotin-Arg-Met¹⁶⁰-Leu-Asn-Asp-Phe-Trp- 332Met¹⁶⁰-Leu-Asn-Asp-Phe-Trp-Ala-Cit-Leu- 333 IV-1Ala-Cit-Leu-Leu-Glu-Arg-Met-Phe-Cit-Leu-Glu-Arg-Met-Phe-Cit-Leu-Val-Asn-Leu-Val-Asn-Ser-Gln-Tyr-His¹⁸¹-Gly-NH₂ Ser-Gln-Tyr-His¹⁸¹ Glypican-Biotin-Gly-Leu²⁰⁷-Lys-Leu-Gln-Val-Thr- 334Leu²⁰⁷-Lys-Leu-Gln-Val-Thr-Cit-Ala-Phe- 335 IV-2Cit-Ala-Phe-Val²¹⁶-Thr²¹²-Arg-Ala-Phe-Val²¹⁶-Thr²¹²-Arg-Ala-Phe-Val-Ala-Ala-Val-Ala-Ala-Cit-Thr-Phe-Ala-Gln²²³-Arg- Cit-Thr-Phe-Ala-Gln²²³ NH₂Glypican- Biotin-Gly-Gly³⁵⁰-Cit-Ile-Ser-Arg-Ser-Ile- 336Gly³⁵⁰-Cit-Ile-Ser-Arg-Ser-Ile-Ser-Glu³⁵⁸- 337 IV-3Ser-Glu³⁵⁸-Gly³⁵⁰-Arg-Ile-Ser-Cit-Ser-Ile-Gly³⁵⁰-Arg-Ile-Ser-Cit-Ser-Ile-Ser-Glu-Ser-Ser-Glu-Ser-Ala-Phe-Ser³⁶²-Arg-NH₂ Ala-Phe-Ser³⁶² Glypican-Biotin-Arg-Leu⁴⁶²-Cit-Gln-Ile-Met-Ala- 338Leu⁴⁶²-Cit-Gln-Ile-Met-Ala-Leu-Arg- 339 IV-4Leu-Arg-Val⁴⁷⁰-Ile⁴⁶⁵-Met-Ala-Leu-Cit-Val⁴⁷⁰-Ile⁴⁶⁵-Met-Ala-Leu-Cit-Val-Met-Thr-Val-Met-Thr-Ser-Lys-Met-Lys⁴⁷⁶-Gly-NH₂ Ser-Lys-Met-Lys⁴⁷⁶ Glypican-V-1Biotin-Gly-Thr⁷⁰-Arg-Lys-Met-Glu-Glu- 340Thr⁷⁰-Arg-Lys-Met-Glu-Glu-Cit-Tyr-Gln- 341Cit-Tyr-Gln-Ile-Ala-Ala-Arg-Gln⁸³-Glu⁷⁵-Ile-Ala-Ala-Arg-Gln⁸³-Glu⁷⁵-Arg-Tyr-Gln-Arg-Tyr-Gln-Ile-Ala-Ala-Cit-Gln-Asp-Met-Ile-Ala-Ala-Cit-Gln-Asp-Met-Gln-Gln⁸⁷ Gln-Gln⁸⁷-Arg-NH₂ Glypican-V-2Biotin-Gly-Ile¹⁹⁴-Arg-Met-Ala-Arg-Cit- 342Ile¹⁹⁴-Arg-Met-Ala-Arg-Cit-Asp-Val-Ser- 343Asp-Val-Ser-Pro-Phe-Gly²⁰⁵-Ala¹⁹⁷-Cit-Pro-Phe-Gly²⁰⁵-Ala¹⁹⁷-Cit-Arg-Asp-Val-Arg-Asp-Val-Ser-Pro-Phe-Gly-Asn-Ile-Pro-Ser-Pro-Phe-Gly-Asn-Ile-Pro-Gln-Cit-Val-Gln-Cit-Val-Met-Gly-Gln²¹⁴-Arg-NH₂ Met-Gly-Gln²¹⁴ Glypican-V-3Biotin-Gly-Lys³³⁶-Leu-Leu-Glu-Gln-Val- 344Lys³³6-Leu-Leu-Glu-Gln-Val-Asn-Cit-Ile- 345Asn-Cit-Ile-Ser-Gly-Cit-Pro-Val-Arg-Thr-Ser-Gly-Cit-Pro-Val-Arg-Thr-Pro-Thr-Pro-Thr-Gln³⁵⁴-Gly³⁴⁶-Arg-Pro-Val-Cit-Gln³⁵⁴-Gly³⁴⁶-Arg-Pro-Val-Cit-Thr-Pro-Thr-Thr-Pro-Thr-Gln-Ser-Pro-Cit-Ser ³⁵⁸-Arg- Gln-Ser-Pro-Cit-Ser ³⁵⁸ NH₂Glypican-V-4 Biotin-Gly-Lys³⁸⁵-Glu-Phe-Ile-Asn-Ser- 346Lys³⁸⁵-Glu-Phe-Ile-Asn-Ser-Leu-Cit-Leu- 347Leu-Cit-Leu-Tyr-Arg-Ser-Phe-Tyr-Gly³⁹⁹-Tyr-Arg-Ser-Phe-Tyr-Gly³⁹⁹-Phe³⁸⁷-Ile-Asn-Phe³⁸⁷-Ile-Asn-Ser-Leu-Arg-Leu-Tyr-Cit-Ser-Leu-Arg-Leu-Tyr-Cit-Ser-Phe-Tyr- Ser-Phe-Tyr-Gly³⁹⁹-Arg-NH₂ Gly³⁹⁹Glypiean- Biotin-Gly-Ser⁹¹-His-Phe-Val-Cit-Thr-Thr- 348Ser⁹¹-His-Phe-Val-Cit-Thr-Thr-Phe-Val- 349 VI-1Phe-Val-Ser-Arg-His¹⁰²-Phe⁹³-Val-Arg-Thr-Ser-Arg-His¹⁰²-Phe⁹³-Val-Arg-Thr-Thr-Phe-Thr-Phe-Val-Ser-Cit-His¹⁰²-Gly-NH₂ Val-Ser-Cit-His¹⁰² Glypican-Biotin-Gly-Lys²⁰⁶-Leu-Lys-Ile-Gln-Val- 350Lys²⁰⁶-Leu-Lys-Ile-Gln-Val-Thr-Cit-Ala- 351 VI-2Thr-Cit-Ala-Phe-Ile-Ala-Ala-Cit-Thr-Phe-Phe-Ile-Ala-Ala-Cit-Thr-Phe-Val-Gln-Gly-Val-Gln-Gly-Leu-Thr-Val-Gly-Cit-Glu-Leu-Thr-Val-Gly-Cit-Glu-Val-Ala-Asn- Val-Ala-Asn-Arg²³⁴-Gly-NH₂ Arg²³⁴Glypican- Biotin-Gly-Thr²²⁶-Val-Gly-Arg-Glu-Val- 352Thr²²⁶-Val-Gly-Arg-Glu-Val-Ala-Asn-Cit- 353 VI-3Ala-Asn-Cit-Val-Ser-Lys-Val-Ser-Pro- Val-Ser-Lys-Val-Ser-Pro-Thr²⁴¹Thr²⁴¹-Arg-NH₂ Glypican- Biotin-Gly-Thr⁴⁵⁴-Arg-Pro-Asp-Thr-Phe- 354Thr⁴⁵⁴-Arg-Pro-Asp-Thr-Phe-Ile-Cit-Gln⁴⁶²- 355 VI-4Ile-Cit-Gln⁴⁶²-Ile⁴⁶⁰-Arg-Gln-Gln-Ile-Met-Ile⁴⁶⁰-Arg-Gln-Gln-Ile-Met-Ala-Leu-Cit-Ala-Leu-Cit-Val-Met-Thr-Asn-Lys-Leu- Val-Met-Thr-Asn-Lys-Leu-Lys⁴⁷⁵Lys⁴⁷⁵-Gly-NH₂

In particular embodiments, one, two, three, four, five, or more (e.g.,all) of the “Cit” (citrulline) residues in any of SEQ ID NOS:40-355shown in Table 8 is replaced with “Arg” (arginine). As one non-limitingexample, the VMT8 core sequence (SEQ ID NO:55) has the following aminoacid sequence: TRSSAVXLRSSVPGVXVRLXSSVPG (SEQ ID NO:400), wherein X=Argor Cit. As another non-limiting example, the VMT7 core sequence (SEQ IDNO:53) has the following amino acid sequence:RSYVTTSTXTYSALRPSTSXSLYATXSSAVRL (SEQ ID NO:401), wherein X=Arg or Cit.As yet another non-limiting example, the VMT13 core sequence (SEQ IDNO:65) has the following amino acid sequence:ANYQDTIGXLDEIATYXKLLEGEESXIS (SEQ ID NO:402), wherein X=Arg or Cit.

Example 7 Synthesis and Testing of Designed Citrullinated Peptides

The present example demonstrates that the heterogeneity in RA can becorrelated to the different autoantibodies against the various synovialproteins present in the patient at different stages of the disease,i.e., early stage, middle stage, and late stage.

The synthetic citrullnated peptides set forth in Example 6, which weredesigned from synovial proteins, were synthesized and evaluated fortheir ability to diagnose and/or prognose RA. Table 9 shows that thesecitrullnated peptides find utility in diagnosing and prognosing variousstages of RA, including early stage, middle stage, and late stage RA.The peptides were then tested for IgG ACPA dose-response in samples ofsynovial fluid taken from both healthy patients and patients with RA.Table 9 shows that many of the synthetic citrillunated peptides derivedfrom synovial protein sequences showed either a strong or moderate IgGACPA dose-response in a sample of synovial fluid from an individual withRA.

TABLE 9 Synthetic citrullinated peptides synthesized and tested for IgGACPA response. Peptides Peptides IgG ACPA Positive RA Protein DesignedSynthesized (Strong/Moderate) Early Stage Vimentin 14 14 3/3 (Initiationof Lamin 21 14 N/A Disease) Bip (P60 Heat 4 4 0/2 (Neutrophil) ShockProtein) Histone 8 8 1/3 β-Actin 1 1 0/0 Myeloblastin 4 4 0/1 PLScramblase 1 1 0/1 Middle Stage Fibrin 24 22 3/4 (Propagation ofApolipoprotein a 9 6 2/0 Disease) (Plasma) Late Stage Collagen 15 15 2/4(Destruction of Syndecan 5 5 0/1 Cartilage & Bone) Fibronectin 12 11 1/4(Matrix) Total Peptides 126 113 12/23

IgG ACPA (anti-citrullinated peptide antibody) dose-response curves ofsynthetic citrullinated peptides derived from Apolipoprotein a werecalculated. FIG. 20 illustrates that several synthesized citrullinatedApolipoprotein a peptides displayed robust binding, as evidenced by theEC50 values calculated for each of the peptides. Significantly, Apo a-4and Apo a-6 both displayed strong IgG ACPA positive responses (i.e.,EC50 values of 1.959 and 3.797, respectively).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from collagen (e.g., Coll.T2α1, Coll.T9α1, Coll.T10α1,Coll.T11α1, Coll.T11α2) were calculated. FIG. 21 illustrates thatseveral synthesized citrullinated collagen peptides displayed robustbinding, as evidenced by the EC50 values calculated for each of thepeptides. Significantly, T9α1-4 and T11α2-1 both displayed strong IgGACPA positive responses (i.e., EC50 values of 7.692 and 7.036,respectively), while T2α1-3, T9α1-1, T10α1-1, and T11α2-4 displayedmoderate IgG ACPA positive responses (i.e., EC50 values of 24.63, 24.90,17.14, and 31.57, respectively).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from vimentin were calculated. FIG. 22 illustrates that severalsynthesized citrullinated vimentin peptides displayed robust binding, asevidenced by the EC50 values calculated for each of the peptides.Significantly, VMT7, VMT8, and VMT13 displayed strong IgG ACPA positiveresponses (i.e., EC50 values of 5.826, 3.639, and 6.020, respectively),while VMT2, VMT6, and VMT14 displayed moderate IgG ACPA positiveresponses (i.e., EC50 values of 21.29, 12.96, and 25.99, respectively).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from fibronectin were calculated. FIG. 23 illustrates thatseveral synthesized citrullinated fibronectin peptides displayed robustbinding, as evidenced by the EC50 values calculated for each of thepeptides. Significantly, FBNT-6 displayed a strong IgG ACPA positiveresponse (i.e., EC50 value of 8.375), while FBNT-3, FBNT-5, FBNT-7, andFBNT-10 displayed moderate IgG ACPA positive responses (i.e., EC50values of 31.04, 21.98, 27.25, and 19.71, respectively).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from fibrin (e.g., fibrin alpha-chain, fibrin beta-chain, fibringamma-chain) were calculated. FIG. 24 illustrates that severalsynthesized citrullinated fibrin peptides displayed robust binding, asevidenced by the EC50 values calculated for each of the peptides.Significantly, FIB-A1, FIB-A8, and FIB-G1 displayed strong IgG ACPApositive responses (i.e., EC50 values of 5.682, 3.030, and 7.863,respectively), while FIB-A3, FIB-A5, FIB-A6, and FIB-B 1 displayedmoderate IgG ACPA positive responses (i.e., EC50 values of 12.19, 25.90,38.12, and 9.207, respectively).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from enolase and syndecan were calculated. FIG. 25 illustratesthat SYNC-IIIa displayed a moderate IgG ACPA positive response (i.e.,EC50 value of 18.93).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from histone, β-actin, and PL scramblase were calculated. FIG.26 illustrates that several of these synthesized citrullinated peptidesdisplayed robust binding, as evidenced by the EC50 values calculated foreach of the peptides. Significantly, H₂B-3 displayed a strong IgG ACPApositive response (i.e., EC50 value of 6.069), while H2A-1, H₂B-2, H3-2,and PL-SCRB displayed moderate IgG ACPA positive responses (i.e., EC50values of 26.43, 21.37, 18.53, and 20.17, respectively).

IgG ACPA dose-response curves of synthetic citrullinated peptidesderived from myeloblastin, BiP, and lamin (e.g., lamin B1, lamin B2,lamin A/C) were calculated. FIG. 27 illustrates that several of thesesynthesized citrullinated peptides displayed robust binding, asevidenced by the EC50 values calculated for each of the peptides.Significantly, MLBS-1, Bip-2, and Bip-3 displayed moderate IgG ACPApositive responses (i.e., EC50 values of 11.20, 22.66, and 22.74,respectively).

As demonstrated in this example, the ability to classify RA patientsinto different stages of the disease will enable the clinician topractice personalized medicine to treat the heterogeneous population ofRA patients with the appropriate medicine at earlier time points andchange the course of the disease. This ability to identifyautoantibodies against each individual citrullinated synovial protein ina patient allows the classification of RA patients into different stagesof the disease.

Example 8 Diagnosing RA Using a Combination of Citrullinated Peptides

The present example demonstrates the development of an assay whichincorporates multiple endogenous synovial protein autoantigens todiagnose, prognose, and/or differentiate RA patients into various stagesfor specialized treatment. Although the specificity for each of thecurrently marketed RA diagnostic assays is good (>90%), none of theassays can achieve a sensitivity of greater than 75%. This discrepancyis due to the fact that the current anti-CCP-based andanti-filaggrin-based assays are not measuring the endogenousautoantigens that are actually present in the synovial joint. Thisexample demonstrates the ability of the present invention to fulfillthis need in the art.

The sensitivity and specificity of RA diagnosis was calculated for asynthesized fibrin citrullinated peptide and three synthesized vimentincitrullinated peptides. Table 10 shows that the sensitivity for RAdiagnosis using the fibrin peptide was 80%, with 100% specificity.Similarly, the VMT2 peptide demonstrated a 75% sensitivity with a 95%specificity. Significantly, when the fibrin and VMT2 peptides were usedin conjunction with each other, 95% sensitivity was achieved.

TABLE 10 Sensitivity and specificity of RA diagnosis using syntheticcitrullinated fibrin and vimentin peptides. Normal Control RA PatientsFibrin VMT1 VMT3 VMT2 Fibrin VMT1 VMT3 VMT2 Sensitivity (%) 80 45 50 75Fibrin + VMT2 95% Sensitivity Specificity (%) 100 95 95 95

It is to be understood that the above description is intended to beillustrative and not restrictive. Many embodiments will be apparent tothose of skill in the art upon reading the above description. The scopeof the invention should, therefore, be determined not with reference tothe above description, but should instead be determined with referenceto the appended claims, along with the full scope of equivalents towhich such claims are entitled. The disclosures of all articles andreferences, including patent applications, patents, PCT publications,Genbank Accession Nos., and Swiss-Prot Accession Nos., are incorporatedherein by reference for all purposes.

What is claimed is:
 1. A method for identifying a peptide that isimmunologically reactive with an anti-citrullinated protein antibody,said method comprising: (a) identifying at least one antigenic peptideepitope in at least one synovial fluid polypeptide, wherein saidantigenic peptide epitope is predicted to be immunologically reactivewith an anti-citrullinated protein antibody, wherein said antigenicpeptide epitope contains at least one arginine residue, and wherein atleast one of said arginine residues is citrullinated; (b) synthesizing apeptide that comprises at least one of said antigenic peptide epitopes;(c) contacting a biological sample from an individual having rheumatoidarthritis (RA) with said peptide under conditions suitable to transformsaid peptide into a complex comprising said peptide and saidanti-citrullinated protein antibody; and (d) identifying said peptide asbeing immunologically reactive with said anti-citrullinated proteinantibody based on the presence or level of said complex.
 2. The methodof claim 1, wherein said at least one synovial fluid polypeptide isselected from the group consisting of vimentin, fibrinogen alpha-chain,fibrinogen beta-chain, fibrinogen gamma-chain, alpha-enolase, β-actin,aggrecan, gelsolin, lumican, fibronectin, tropomyosin, cartilageoligomeric matrix protein, glucose-6-phosphate isomerase, lamin B1,lamin B2, lamin A/C, myeloblastin (proteinase 3), phospholipid (PL)scramblase 1, apolipoprotein (a), BiP (heat shock 70 kDa protein 5),histone H2A, histone H₂B, histone H3, histone H4, COL2A1, COL9A1,COL10A1, COL11A1, COL11A2, syndecan 1, syndecan 3, CD44, intercellularadhesion molecule 1 (ICAM1), vascular cell adhesion molecule 1 (VCAM1),glypican 1, glypican 2, glypican 4, glypican 5, glypican 6, vitronectin,nidogen, and combinations thereof.
 3. The method of claim 1, whereinsaid antigenic peptide epitope comprises at least 9 contiguous aminoacids of said synovial fluid polypeptide sequence.
 4. The method ofclaim 1, wherein said antigenic peptide epitope is predicted to beimmunologically reactive with an anti-citrullinated protein antibodywhen a score calculated for said antigenic peptide epitope is greaterthan or equal to a predetermined score.
 5. The method of claim 4,wherein said score for said antigenic peptide epitope is calculated byadding up a value given to each amino acid in said antigenic peptideepitope based on the position and side-chain of said amino acid.
 6. Themethod of claim 5, wherein said value given to each amino acid at aparticular position (P 1-P9) in said antigenic peptide epitope is shownin FIG.
 10. 7. The method of claim 4, wherein said predetermined scoreis +2.0.
 8. The method of claim 1, wherein said sample is human serum.9. The method of claim 1, wherein step (b) comprises synthesizing apeptide that comprises at least two of said antigenic peptide epitopes,wherein said antigenic peptide epitopes are linked together by a peptidebond.
 10. The method of claim 1, wherein step (b) comprises synthesizinga peptide that comprises three of said antigenic peptide epitopes,wherein said antigenic peptide epitopes are linked together by a peptidebond.
 11. The method of claim 1, wherein said complex in step (c) isdetected with a detectable moiety conjugated to said peptide.
 12. Themethod of claim 11, wherein said detectable moiety is a fluorescentmoiety.
 13. The method of claim 1, wherein step (c) comprises thesub-steps of: (i) contacting said complex with a detection reagentcomprising a reporter group to transform said complex into a labeledcomplex; and (ii) detecting the presence or level of said labeledcomplex.
 14. The method of claim 13, wherein said detection reagent isselected from the group consisting of an anti-IgA antibody, an anti-IgGantibody, an anti-IgM antibody, Protein L, Protein A, Protein G, andmixtures thereof.
 15. The method of claim 13, wherein said reportergroup is selected from the group consisting of radioactive groups,fluorescent groups, luminescent groups, enzymes, biotin, and dyes. 16.The method of claim 13, wherein detecting the presence or level of saidlabeled complex comprises detecting the presence or level of a signalgenerated from said reporter group.
 17. The method of claim 16, whereindetecting the presence or level of a signal generated from said reportergroup comprises the use of a detection device.
 18. The method of claim17, wherein said detection device comprises a spectrophotometer.
 19. Themethod of claim 1, wherein said anti-citrullinated protein antibodycomprises an IgA anti-citrullinated protein antibody, IgGanti-citrullinated protein antibody, IgM anti-citrullinated proteinantibody, or mixtures thereof.
 20. The method of claim 1, wherein step(c) comprises an enzyme-linked immunosorbent assay (ELISA), afluorescence polarization assay, or a fluorescence anisotropy assay. 21.A synthetic peptide identified by the method of claim
 1. 22. Thesynthetic peptide of claim 21, wherein said peptide is about 15 to about40 amino acids in length.
 23. The synthetic peptide of claim 21, whereinsaid peptide further comprises a tag.
 24. The synthetic peptide of claim23, wherein said tag is biotin.
 25. A kit comprising: (a) at least onesynthetic peptide identified by the method of claim 1; and (b) adetection reagent comprising a reporter group.
 26. The kit of claim 25,wherein said at least one synthetic peptide is immobilized on a solidsupport.
 27. The kit of claim 25, wherein said detection reagent isselected from the group consisting of an anti-IgA antibody, an anti-IgGantibody, an anti-IgM antibody, Protein L, Protein A, Protein G, andmixtures thereof.
 28. The kit of claim 25, wherein said reporter groupis selected from the group consisting of radioactive groups, fluorescentgroups, luminescent groups, enzymes, biotin, and dyes.